Habitat biodiversity as a determinant of fish community structure on coral reefs

Increased habitat diversity is often predicted to promote the diversity of animal communities because a greater variety of habitats increases the opportunities for species to specialize on different resources and coexist. Although positive correlations between the diversities of habitat and associated animals are often observed, the underlying mechanisms are only now starting to emerge, and none have been tested specifically in the marine environment. Scleractinian corals constitute the primary habitat-forming organisms on coral reefs and, as such, play an important role in structuring associated reef fish communities. Using the same field experimental design in two geographic localities differing in regional fish species composition, we tested the effects of coral species richness and composition on the diversity, abundance, and structure of the local fish community. Richness of coral species overall had a positive effect on fish species richness but had no effect on total fish abundance or evenness. At both localities, certain individual coral species supported similar levels of fish diversity and abundance as the high coral richness treatments, suggesting that particular coral species are disproportionately important in promoting high local fish diversity. Furthermore, in both localities, different microhabitats (coral species) supported very different fish communities, indicating that most reef fish species distinguish habitat at the level of coral species. Fish communities colonizing treatments of higher coral species richness represented a combination of those inhabiting the constituent coral species. These findings suggest that mechanisms underlying habitat-animal interaction in the terrestrial environment also apply to marine systems and highlight the importance of coral diversity to local fish diversity. The loss of particular key coral species is likely to have a disproportionate impact on the biodiversity of associated fish communities.     

Consequences of patch reef spacing for density-dependent mortality of coral-reef fishes

The spatial configuration of habitat patches can profoundly affect a number of ecological interactions, including those between predators and prey. I examined the effects of reef spacing on predator-prey interactions within coral-reef fish assemblages in the Bahamas. Using manipulative field experiments, I determined that reef spacing influences whether and how density-dependent predation occurs. Mortality rates of juveniles of two ecologically dissimilar species (beaugregory damselfish and yellowhead wrasse) were similarly affected by reef spacing; for both species, mortality was density dependent on reef patches that were spatially isolated (separated by 50 m), and density independent on reef patches that were aggregated (separated by 5 m). A subsequent experiment with the damselfish demonstrated that a common resident predator (coney) caused a substantial proportion of the observed mortality, independent of reef spacing. Compared to isolated reefs, aggregated reefs were much more likely to be visited by transient predators (mostly yellowtail snappers), regardless of prey density, and on these reefs, mortality rates approached 100% for both prey species. Transient predators exhibited neither an aggregative response nor a type 3 functional response, and consequently were not the source of density dependence observed on the isolated reefs. These patterns suggest that resident predators caused density-dependent mortality in their prey through type 3 functional responses on all reefs, but on aggregated reefs, this density dependence was overwhelmed by high, density-independent mortality caused by transient predators. Thus, the spatial configuration of reef habitat affected both the magnitude of total predation and the existence of density-dependent mortality. The combined effects of the increasing fragmentation of coral reef habitats at numerous scales and global declines in predatory fish may have important consequences for the regulation of resident fish populations.     

The influence of resource specialization on the response of reef fish to coral disturbance

Ecological theory predicts that habitat generalists are less prone to decline or extinction in response to habitat disturbance than habitat specialists. One mechanism that may afford habitat generalists greater persistence is their ability to successfully emigrate from degrading environments. This study compared the response of habitat specialist and generalist reef fish species to live coral disturbance. In replicate coral colonies, live coral was experimentally degraded (low, medium and high coral loss). Species continued residence within the colonies was then surveyed over time. In addition, the ability of habitat generalist and specialist species to migrate between degraded (100% loss) and live coral colonies was compared. Habitat specialists exhibited a higher propensity to remain in colonies with low levels of coral loss. However, there was no significant difference between specialist and generalist species in continued residence in habitats with either medium or high levels of coral loss; both functional groups showed low levels of residence. In terms of migration success, generalists moved further than specialists and showed higher levels of successful migration over the majority of distances examined. The influence of habitat specialization on the behavioral response to coral loss may be a useful predictor of changes to coral reef fish communities in response to coral disturbance.     

Fish Responses to Experimental Fragmentation of Seagrass Habitat

Abstract: Understanding the consequences of habitat fragmentation has come mostly from comparisons of patchy and continuous habitats. Because fragmentation is a process, it is most accurately studied by actively fragmenting large patches into multiple smaller patches. We fragmented artificial seagrass habitats and evaluated the impacts of fragmentation on fish abundance and species richness over time (1 day, 1 week, 1 month). Fish assemblages were compared among 4 treatments: control (single, continuous 9‐m² patches); fragmented (single, continuous 9‐m² patches fragmented to 4 discrete 1‐m² patches); prefragmented/patchy (4 discrete 1‐m² patches with the same arrangement as fragmented); and disturbance control (fragmented then immediately restored to continuous 9‐m² patches). Patchy seagrass had lower species richness than actively fragmented seagrass (up to 39% fewer species after 1 week), but species richness in fragmented treatments was similar to controls. Total fish abundance did not vary among treatments and therefore was unaffected by fragmentation, patchiness, or disturbance caused during fragmentation. Patterns in species richness and abundance were consistent 1 day, 1 week, and 1 month after fragmentation. The expected decrease in fish abundance from reduced total seagrass area in fragmented and patchy seagrass appeared to be offset by greater fish density per unit area of seagrass. If fish prefer to live at edges, then the effects of seagrass habitat loss on fish abundance may have been offset by the increase (25%) in seagrass perimeter in fragmented and patchy treatments. Possibly there is some threshold of seagrass patch connectivity below which fish abundances cannot be maintained. The immediate responses of fish to experimental habitat fragmentation provided insights beyond those possible from comparisons of continuous and historically patchy habitat.     

Importance of macroalgal fields as coral reef fish nursery habitat in north-west Australia

Macroalgal fields are a feature of the shallow tropical benthos, yet their importance for coral reef fish population dynamics remains poorly understood. The abundance of fish recruits was recorded using underwater visual census at six macroalgal and 11 coral reef sites in the Montebello and Barrow Islands. Surveys identified 6,935 individual recruit fish from 105 species, 54 genera and 20 families. Of these, 1,401 recruits from 48 species, 31 genera and 14 families were observed in macroalgal sites. Sixteen of the 105 recruit species (15.2 %) were observed exclusively at macroalgal sites. Forty-two (87.5 %) of these species have been observed as adults on adjacent coral reefs. Species composition of fish recruits differed significantly between the two habitats. Corallivore, small omnivore and zooplanktivore recruits had significantly higher numbers in the coral sites, while the results clearly demonstrate that juveniles, within the genera Lethrinus and Choerodon, as well as large algal croppers, are predominantly found at macroalgal (74–100 %) rather than coral-dominated sites. High-canopy macroalgae cover was positively correlated with abundance of these taxa, particularly Lethrinids (r ² = 0.40). This study is the first to highlight the important attributes of tropical macroalgal fields and suggests that they have a similar role to seagrass meadows as essential juvenile habitat, thus warranting greater attention in conservation planning and ecological studies.     

Diversity,abundance, and distribution of reef sharks on outer-shelf reefs of the Great Barrier Reef,Australia

Quantifying the distribution and habitat use of sharks is critical for understanding their ecological role and for establishing appropriate conservation and management regimes. On coral reefs, particularly the Great Barrier Reef (GBR), little is known regarding the distribution of sharks across major reef habitat types. In this study, we surveyed shark populations across outer-shelf reefs of the GBR in order to determine the diversity, abundance, and distribution of reef sharks across three major coral reef habitats: (1) the reef slope, (2) the back reef and (3) the reef flat. Model selection revealed that habitat was the principal factor influencing shark distribution and abundance. Specifically, overall shark abundance and diversity were significantly higher on the reef slope (and to a lesser degree, the back reef) than the reef flat. This confirms that shark populations are not homogeneously distributed across coral reefs. Thus, the results presented herein have important implications for shark population assessments. In addition, our results highlight the potential importance of the reef slope, with high levels of live coral cover and structural complexity, for sustaining reef shark populations. As this habitat is highly susceptible to disturbance events, this study provides a useful context for predicting and understanding how environmental degradation may influence reef shark populations in the future.     

Motile cryptofauna associated with live and dead coral substrates: implications for coral mortality and framework erosion

Coral reef cryptofauna are a diverse group of metazoan taxa that live within intra- and inter-skeletal voids formed by framework structures. Despite a hypothesized high biomass and numerous trophic roles, they remain uncharacterized relative to exposed reef communities. Motile cryptofauna were sampled from live coral colonies and dead frameworks typifying four successive levels of degradation on an eastern Pacific pocilloporid reef. Abundances and biomass were higher on live versus dead corals habitats. The density of cryptofauna per volume substrate was highest on dead coral frameworks of intermediate degradation, where complex eroded substrates provide abundant shelters. These data have important and far-reaching ramifications for how the diverse multispecies assemblages that are reef ecosystems will respond to anthropogenic stressors such as those associated with climate change. Extreme levels of coral mortality, bioerosion, and habitat destruction will lead to impairment and eventually loss of ecosystem functions.     

Spatial and temporal variation in coral recruitment on the Great Barrier Reef: Implications for dispersal hypotheses

Over 15 000 coral recruits were counted on settlement plates from three mid-shelf reefs and six fringing reefs in the northern section of the Great Barrier Reef during two summers (1986 and 1987) and one winter (1987). The density of coral recruits on some settlement plates from a fringing reef was up to 4.88 cm^–2, the highest value ever reported. Mean density of recruits was greater on fringing reefs (81.1 recruits/settlement plate) than on mid-shelf reefs (15.6 recruits/settlement plate), but there was greater spatial variation in abundance of recruits between the fringing reef sites. Other differences between the mid-shelf reefs and the fringing reefs were that different taxa were dominant, and that settlement orientation differed, with mid-shelf recruits settling preferentially on horizontally oriented surfaces and fringingreef recruits preferring vertical surfaces. Of the three midshelf reefs, Green Island reef recorded the highest recruitment rate for each of the two summers, despite having a depauperate adult coral population following predation by the asteroidAcanthaster planci. This suggests that coral larvae frequently travel between reefs. In contrast with an earlier study, there was no consistent difference in abundance of recruits between forereef and backreef locations. Overall, the results indicated great spatial variation in the availability of coral larvae, both on the scale of whole reefs and within-reef habitats.     

Relative influence of environmental factors and fishing on coral reef fish assemblages

Understanding whether assemblages of species respond more strongly to bottom-up (availability of trophic resources or habitats) or top-down (predation pressure) processes is important for effective management of resources and ecosystems. We determined the relative influence of environmental factors and predation by humans in shaping the density, biomass, and species richness of 4 medium-bodied (10–40 cm total length [TL]) coral reef fish groups targeted by fishers (mesopredators, planktivores, grazer and detritivores, and scrapers) and the density of 2 groups not targeted by fishers (invertivores, small fish ≤10 cm TL) in the central Philippines. Boosted regression trees were used to model the response of each fish group to 21 predictor variables: 13 habitat variables, 5 island variables, and 3 fishing variables (no-take marine reserve [NTMR] presence or absence, NTMR size, and NTMR age). Targeted and nontargeted fish groups responded most strongly to habitat variables, then island variables. Fishing (NTMR) variables generally had less influence on fish groups. Of the habitat variables, live hard coral cover, structural complexity or habitat complexity index, and depth had the greatest effects on density, biomass, and species richness of targeted fish groups and on the density of nontargeted fishes. Of the island variables, proximity to the nearest river and island elevation had the most influence on fish groups. The NTMRs affected only fishes targeted by fishers; NTMR size positively correlated with density, biomass, and species richness of targeted fishes, particularly mesopredatory, and grazing and detritivorous fishes. Importantly, NTMRs as small as 15 ha positively affected medium-bodied fishes. This finding provides reassurance for regions that have invested in small-scale community-managed NTMRs. However, management strategies that integrate sound coastal land-use practices to conserve adjacent reef fish habitat, strategic NTMR placement, and establishment of larger NTMRs will be crucial for maintaining biodiversity and fisheries.     

Is habitat amount important for biodiversity in rocky shore systems? A study of South African mussel assemblages

Habitat-forming species on rocky shores are often subject to high levels of exploitation, but the effects of subsequent habitat loss and fragmentation on associated species and the ecosystem as a whole are poorly understood. In this study, the effects of habitat amount on the fauna associated with mussel beds were investigated, testing for the existence of threshold effects at small landscape scales. Specifically, the relationships between mussel or algal habitat amount and: associated biodiversity, associated macrofaunal abundance and density of mussel recruits were studied at three sites (Kidd’s Beach, Kayser’s Beach and Kini Bay) on the southern and south-eastern coasts of South Africa. Samples, including mussel-associated macrofauna, of 10 × 10 cm were taken from areas with 100 % mussel cover (Perna perna or a combination of P. perna and Mytilus galloprovincialis) at each site. The amount of habitat provided by mussels and algae surrounding the sampled areas was thereafter determined at the 4.0 m² scale. A number of significant positive relationships were found between the amount of surrounding mussel habitat and the abundances of several taxa (Anthozoa, Malacostraca and Nemertea). Likewise, there were positive relationships between the amount of surrounding algal habitat and total animal abundance as well as abundance of mussel recruits at one site, Kini Bay. In contrast, abundance of mussel recruits showed a significant negative relationship with the amount of mussel habitat at Kayser’s Beach. Significant negative relationships were also detected between the amount of mussel habitat and species richness and total abundance at Kidd’s Beach, and between amount of mussel habitat and the abundance of many taxa (Bivalvia, Gastropoda, Maxillopoda, Ophiuroidea, Polychaeta and Pycnogonida) at all three sites. No threshold effects were found, nor were significant relationships consistent across the investigated sites. The results indicate that the surrounding landscape is important in shaping the structure of communities associated with these mussel beds, with significant effects of the amount of surrounding habitat per se. The strength and the direction of habitat effects vary, however, between shores and probably with the scale of observation as well as with the studied dependent variables (e.g. diversity, abundance, mussel recruitment, species identity), indicating the complexity of the processes structuring macrofaunal communities on these shores.     

Effects of Patch Size on Birds in Old-Growth Montane Forests

Following habitat alteration or fragmentation, competition, parasitism, and predation from species that live in the new habitats may reduce the survival and reproductive success of species living in the original habitats. Negative influences from species that live outside the remnant patches are expected to be greater in small rather than in large remnant patches because more "external" species are expected to move through the centers of small remnant patches. We surveyed birds within remnant patches of old-growth montane forests on Vancouver Island, Canada, (1) to evaluate whether the richness and abundance of non-old-growth bird species were larger at the center of small rather than large patches and (2) to evaluate whether the opposite was true of old-growth bird species. More non-old-growth bird species were present at the center of small remnant patches of old growth than in large old-growth patches. We found no relationship, however, between patch size and richness or abundance of old-growth bird species at the center of remnant patches of old growth. This was true for old-growth species with open, cup-shaped nests and cavity nests. Old-growth birds may have been affected less in our study area than in other areas because they evolved within heterogeneous montane forests and interacted with non-old-growth species throughout their evolutionary histories or because the contrast between old-growth forests and logged areas was less than that between the forests and agricultural/urban areas that were surveyed in other studies.     

Meta-analysis of the differential effects of habitat fragmentation and degradation on plant genetic diversity

Genetic diversity is a key factor for population survival and evolution. However, anthropogenic habitat disturbance can erode it, making populations more prone to extinction. Aiming to assess the global effects of habitat disturbance on plant genetic variation, we conducted a meta-analysis based on 92 case studies obtained from published literature. We compared the effects of habitat fragmentation and degradation on plant allelic richness and gene diversity (equivalent to expected heterozygosity) and tested whether such changes are sensitive to different life-forms, life spans, mating systems, and commonness. Anthropogenic disturbance had a negative effect on allelic richness, but not on gene diversity. Habitat fragmentation had a negative effect on genetic variation, whereas habitat degradation had no effect. When we examined the individual effects in fragmented habitats, allelic richness and gene diversity decreased, but this decrease was strongly dependent on certain plant traits. Specifically, common long-lived trees and self-incompatible species were more susceptible to allelic richness loss. Conversely, gene diversity decreased in common short-lived species (herbs) with self-compatible reproduction. In a wider geographical context, tropical plant communities were more sensitive to allelic richness loss, whereas temperate plant communities were more sensitive to gene diversity loss. Our synthesis showed complex responses to habitat disturbance among plant species. In many cases, the absence of effects could be the result of the time elapsed since the disturbance event or reproductive systems favoring self-pollination, but attention must be paid to those plant species that are more susceptible to losing genetic diversity, and appropriate conservation should be actions taken.     

Evaluating Effects of Habitat Loss and Land-Use Continuity on Ant Species Richness in Seminatural Grassland Remnants

Abstract:  Seminatural grasslands in Europe are susceptible to habitat destruction and fragmentation that result in negative effects on biodiversity because of increased isolation and area effects on extinction rate. However, even small habitat patches of seminatural grasslands might be of value for conservation and restoration of species richness in a landscape with a long history of management, which has been argued to lead to high species richness. We tested whether ant communities have been negatively affected by habitat loss and increased isolation of seminatural grasslands during the twentieth century. We examined species richness and community composition in seminatural grasslands of different size in a mosaic landscape in Central Sweden. Grasslands managed continuously over centuries harbored species-rich and ecologically diverse ant communities. Grassland remnant size had no effect on ant species richness. Small grassland remnants did not harbor a nested subset of the ant species of larger habitats. Community composition of ants was mainly affected by habitat conditions. Our results suggest that the abandonment of traditional land use and the encroachment of trees, rather than the effects of fragmentation, are important for species composition in seminatural grasslands. Our results highlight the importance of considering land-use continuity and dispersal ability of the focal organisms when examining the effects of habitat loss and fragmentation on biodiversity. Landscape history should be considered in conservation programs focusing on effects of land-use change.     

Appraisal of visual assessments of habitat complexity and benthic composition on coral reefs

Visual assessments of topographic habitat structure and benthos on coral reefs were appraised using quantitative data collected from 16 replicate surveys within each of 21 sites on Seychelles reefs. Results from visual assessments of reef benthos were similar to those obtained using techniques frequently used to assess benthic complexity and composition. Visual estimates of habitat topography were correlated with rugosity, reef height and holes of 10–70 cm diameter, whilst visual estimates of benthic composition were very similar to those obtained from line intercept transects. Visual estimates of topography correlated strongly with species richness of fish communities and explained 42% of the variation in these data. The relationship between visual estimates of topography and species richness is strongest with fish 10–30 cm total length (TL), abundance of fish within this size category also correlating positively with topographic visual assessments. Visual techniques are prone to observer bias, however with regular training they can be used to quickly provide a reliable and effective means of assessing habitat complexity and benthos on coral reefs.     

How well do sunken vessels approximate fish assemblages on coral reefs? Conservation implications of vessel-reef deployments

The amount of artificial habitat (termed ??artificial reef??, AR) in marine systems is rapidly increasing, yet the effect of most types of AR on reef communities remains unknown. We examined the role of well-established vessel-reefs in structuring coral reef fish assemblages by comparing assemblages on 7 World War II wrecks (>65?years old) to those on interspersed coral patch reefs of comparable size in a tropical lagoon. Fish abundance, species richness, diversity and feeding guild structure on wrecks were similar to natural reefs; however, species composition differed between the two reef types (R?=?0.189?C0.341, average dissimilarity: 67.3?C68.8?%). Despite being more species-rich and diverse, fish assemblages on larger wrecks were less similar to assemblages on their adjacent natural reefs than smaller wrecks. Wrecks may also have affected fish abundance on adjacent natural reefs, with reefs adjacent to larger wrecks supporting higher abundances than reefs adjacent to smaller wrecks. Our results indicate that increases in vessel-reef habitat may not greatly affect reef fish assemblage parameters, but may affect the relative abundances of particular species.     

Habitat modification affects recruitment of abalone in central New Zealand

The habitat experienced during early life-history stages can determine the number and quality of individuals that recruit to adult populations. In a field experiment, biogenic habitat complexity was manipulated (presence or absence of foliose macroalgae) at two depths (2–3 m and 5–6 m) and the habitat-dependent effects on recruitment of the black foot abalone (Haliotis iris) were examined at three field sites along the south coast of Wellington, New Zealand (41°20′S, 174°47′E), between July and November 2005. Recruit density (<5 weeks post-settlement) was measured on cobbles covered with crustose coralline algae. Habitats of low complexity (barrens treatments) had consistently greater densities of recruits than habitats of high complexity (algae treatments). However, recruits in algae habitats were larger, and for deep habitats, there was greater survival in algae habitats compared with barrens habitats. While depth had no significant effect on early recruit (<2 weeks post-settlement) density, late recruit (<5 weeks post-settlement) density was greater in shallow habitats, and so it seems recruit survival was greater in shallow habitats. In this experiment, algal habitat complexity had strong effects on early recruit abundance, but habitat-dependent variations in recruit growth and survival may modify initial patterns of abundance and determine recruitment to adult abalone populations.     

The basics of acidification: baseline variability of pH on Australian coral reefs

Ocean acidification is one of the key threats facing coral reef ecosystems, but there are few estimates of spatial and temporal variability in pH among reef habitats. The present study documents levels of spatial variability in pH among coral reef habitats (9 to 10), among locations separated by 100’s km of latitude and between east (Great Barrier Reef, GBR) and west (Ningaloo Reef) coasts of Australia. Differences were found in pH between inshore and offshore waters along Ningaloo Reef (means 8.45, 8.53, respectively). Replicate assessments here ranged from 8.22 to 8.64. On the GBR, the range of values over all habitats and replicates was 0.39 pH units (7.98 to 8.37). There were minor but significant differences of 0.05 pH units between 5 consecutive days for habitats on average. Highest pH was recorded in filamentous algal beds maintained by the damselfish Dischistodus perspicillatus. Lowest pH was found in water extracted from sand-dwelling goby holes. While there were marked changes in pH over a 48-h sampling period among 4 habitats at Lizard Island (GBR), there was little evidence of a diel trend. Understanding how pH varies at scales that are relevant to organisms that live on shallow coral reefs is crucial for the design and interpretation of experiments that test the effects on organisms of the changes in water chemistry predicted to affect oceans in the future.     

Acute effects of removing large fish from a near-pristine coral reef

Large animals are severely depleted in many ecosystems, yet we are only beginning to understand the ecological implications of their loss. To empirically measure the short-term effects of removing large animals from an ocean ecosystem, we used exclosures to remove large fish from a near-pristine coral reef at Palmyra Atoll, Central Pacific Ocean. We identified a range of effects that followed from the removal of these large fish. These effects were revealed within weeks of their removal. Removing large fish (1) altered the behavior of prey fish; (2) reduced rates of herbivory on certain species of reef algae; (3) had both direct positive (reduced mortality of coral recruits) and indirect negative (through reduced grazing pressure on competitive algae) impacts on recruiting corals; and (4) tended to decrease abundances of small mobile benthic invertebrates. Results of this kind help advance our understanding of the ecological importance of large animals in ecosystems.     

Sponge-feeding by the Caribbean starfish Oreaster reticulatus

The common Caribbean starfish Oreaster reticulatus (Linnaeus) feeds on sponges by everting its stomach onto a sponge and digesting the tissue, leaving behind the sponge skeleton. In the San Blas Islands, Republic of Panama, 54.2% of the 1549 starfish examined from February 1987 to June 1990 at eight sites were feeding, and 61.4% of these were feeding on sponges, representing 51 species. Sponges were fed on disproportionately heavily in comparison to their abundance, which was only 9.7% of available prey. In feeding choice experiments, 736 pieces of 34 species of common sponges from a variety of shallow-water habitats, and also 9 ind of a coral, were offered to starfish in individual underwater cages. Acceptance or rejection of sponge species was unambiguous for 31 of the 34 species, and there was a clear relationship between sponge acceptability and sponge habitat. Starfish ate 16 of 20 species that normally grow only on the reefs, but only 1 of 14 species that live in the seagrass meadows and rubble flats surrounding the reefs. The starfish live in the seagrass meadows and rubble flats, and avoid the reefs, and so the acceptable reef sponges are generally inaccessible until a storm fragments and transports them into starfish habitat. After Huricane Joan washed fragments of reef sponges into a seagrass meadow in October 1988, starfish consumed the edible species. When the seagrass meadow was experimentally seeded with tagged reef sponge fragments in June 1994, O. reticulatus consumed edible species and accumulated in the area seeded. Reef sponges that were living in a seagrass meadow, from which O. reticulatus had been absent for at least 4 yr (from 1978 to 1982), were eliminated when the starfish migrated into the area, and the sponges have been unable to recolonize up to June 1994. O. reticulatus feeding and habitat preferences appear to restrict distributions of many Caribbean reef sponge species to habitats without O. reticulatus and may have exerted significant selective pressure on defences of those sponges that live in O. reticulatus habitats.     

Defining Critical Habitats of Threatened and Endemic Reef Fishes with a Multivariate Approach

Understanding critical habitats of threatened and endemic animals is essential for mitigating extinction risks, developing recovery plans, and siting reserves, but assessment methods are generally lacking. We evaluated critical habitats of 8 threatened or endemic fish species on coral and rocky reefs of subtropical eastern Australia, by measuring physical and substratum‐type variables of habitats at fish sightings. We used nonmetric and metric multidimensional scaling (nMDS, mMDS), Analysis of similarities (ANOSIM), similarity percentages analysis (SIMPER), permutational analysis of multivariate dispersions (PERMDISP), and other multivariate tools to distinguish critical habitats. Niche breadth was widest for 2 endemic wrasses, and reef inclination was important for several species, often found in relatively deep microhabitats. Critical habitats of mainland reef species included small caves or habitat‐forming hosts such as gorgonian corals and black coral trees. Hard corals appeared important for reef fishes at Lord Howe Island, and red algae for mainland reef fishes. A wide range of habitat variables are required to assess critical habitats owing to varied affinities of species to different habitat features. We advocate assessments of critical habitats matched to the spatial scale used by the animals and a combination of multivariate methods. Our multivariate approach furnishes a general template for assessing the critical habitats of species, understanding how these vary among species, and determining differences in the degree of habitat specificity. Definición de Hábitats Críticos para Peces Arrecifales Amenazados y Endémicos Mediante un Método Multivariado