Reef-fish community structure and habitat associations are well documented for shallow coral reefs (<20 m) but are largely unknown in deeper extensions of reefs (mesophotic reefs; >30 m). We documented the community structure of fishes and seafloor habitat composition through visual observations at depth intervals from 3 to 50 m in West Hawaii. Community structure changed gradually with depth, with more than 78% of fish species observed at mesophotic depths also found in shallow reef habitats. Depth explained 17% of the variation in reef-fish community structure; live coral cover explained 10% and prevalence of sand accounted for 7% of the fitted variation indicating that depth-related factors and coral habitat play a predominant role in structuring these communities. Differences in community structure also appear to be linked closely with feeding behavior. Trophic designation accounted for 31% of the fitted variation, with changes in herbivore abundance accounting for 10% of the variation. These findings suggest that changes in reef-fish community composition from shallow to mesophotic environments are largely influenced by trophic position, coral habitat and indirect effects of depth itself.