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The mechanisms that govern fauna-habitat associations across multiple spatial scales remain largely undefined. Can environmental factors structure fauna-habitat associations over both local and global spatial scales, alongside biogeographical processes and patterns? We compare the extent to which the use of mangroves by fishes is consistent within and between biogeographic locations, and whether any similarities and differences can be attributed to the environmental context of those forests, such as the physical environment, seascape composition and constraints on access by fishes. We focus on three important proxies of these structuring forces for fish—salinity, distance to reefs and tidal amplitude. Using directly comparable remote underwater visual census from a range of diverse environmental contexts in the Central and Eastern Indo-Pacific, we examine similarity in the family-level taxonomic composition of fish assemblages in mangrove forests. Local environmental context appears to explain similarities and differences in mangrove association by fishes at both regional and local scales across the Indo-Pacific. There were strong consistencies in taxonomic composition in similar environmental contexts despite geographic separation. Tidal amplitude was a powerful explanatory factor that interacted with both distance to reef and salinity in partitioning variation in fish assemblage structure. Substantial differences in the use of mangroves between regions appear to be independent of historical biogeography, relating instead to local context. Our findings suggest that the effects of local context on habitat suitability can play out over biogeographical scales, and global similarities in fauna-habitat associations may be partially explained by comparable environmental contexts, with important management implications.

Genetic diversity and connectivity are key factors in determining a population’s resilience to future disturbance. This is especially relevant to corals, which are in global decline due to increasing frequency and strength of thermal anomalies and severe tropical cyclones. While many studies have investigated genetic diversity and population structure in corals, they focused on species being removed at the greatest rate from coral reefs, acroporids and pocilloporids, and it is unclear whether the patterns observed in these species reflects those found in more resilient species. Here, we use microsatellite markers and two Lagrangian models with differing resolutions, to investigate population structure in a stress-tolerant coral survivor Cyphastrea microphthalma, Family Merulinidae, along the north-western Australian coastline. We found evidence of four genetic clusters with some level of admixture among them. However, while there was evidence of population structure within the intensively sampled Pilbara region, the patterns of connectivity differed to those reported previously. WA populations of C. microphthalma were also characterised by lower levels of genetic diversity at higher latitudes. High- and moderate-resolution Lagrangian models did not significantly predict regional-scale genetic connectivity across the Pilbara and Ningaloo (500 km). Although the high-resolution model explained an order of magnitude more genetic variation, suggesting model resolution and resolving coastal processes are important. Over broad spatial scales (nearly 2000 km), all moderate-resolution model particle release durations significantly predicted the genetic differentiation, although over-water distance best-predicted the genetic distance across this spatial scale. This study improves the understanding of connectivity in this region by focusing on a stress-tolerant species incorporating a spatially more intensive sampling effort than previous coral studies. It also shows that further development of Lagrangian models is required, such as inclusion of multi-generational stepwise models and larval behaviour, to improve predictions of connectivity for this coral species in this region.