Mesophotic coral reef ecosystems, typically occurring between 30 and 150 m depth, are increasingly recognised as important habitats that support marine biodiversity and ecosystem function. Although movement of some fish species between shallow and mesophotic reefs suggests ecological connectivity, differences in fish community composition across depth gradients and the extent of connectivity between these habitats remain poorly understood. This study characterised fish assemblages from six coral reef mesophotic habitats (coral, Cycloseris-dominated beds, macroalgae, rhodolith, sand and sponge) encountered between 14 and 74 m depths in the northern Ningaloo Marine Park, Western Australia. From 111 Baited Remote Underwater stereo-Video system (stereo-BRUVs) deployments, we recorded 13,541 individuals from 297 species. Fish assemblage composition differed significantly between habitats with coral, sponge and sand habitats supporting the most distinct communities. Coral habitats had the highest number of species and fish while sand habitats consistently supported the lowest number of species. Depth, benthic habitat type and location explained up to 45.6% of the variation in the fish assemblage composition by abundance, and 43.2% in the composition by biomass. Fish body sizes also varied significantly across habitats, with larger individuals found in sand habitats and smaller individuals observed in sponge and Cycloseris habitats. Depth-related shifts in trophic structure were also evident, with lower trophic consumers declining with depth and apex predators becoming proportionally more abundant in deeper or less structurally complex habitats. Coral and sponge habitats supported higher abundances and biomasses of ecologically important and recreationally targeted species, such as the coral trout (Plectropomus spp.), emperor (Lethrinus atkinsoni) and butterflyfish (Chaetodon assarius). These findings highlight the ecological complexity and habitat-specificity of mesophotic fish communities and highlight the need to incorporate structurally diverse deep reef habitats into marine spatial planning.
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