Coral community composition varies considerably due to both environmental conditions and disturbance histories. However, the extent to which coral composition influences associated fish assemblages remains largely unknown. Here an ecological trait-based ordination analysis was used to compare functional richness (range of unique trait combinations), functional evenness (weighted distribution of fishes with shared traits), and functional divergence (proportion of total abundance supported by species with traits on the periphery of functional space) of fish assemblages among six distinct coral habitats. Despite no significant variation in species richness among habitats, there were differences in the functional richness and functional divergence, but not functional evenness, of fish assemblages among habitats. Structural complexity of coral assemblages was the best predictor of the differences in functional richness and divergence among habitats. Functional richness of fish assemblages was highest in branching Porites habitats, lowest in Pocillopora and soft coral habitats, and intermediate in massive Porites, staghorn Acropora, and mixed coral habitats. Massive and branching Porites habitats displayed greater functional divergence in fish assemblages than the Pocillopora habitat, whilst the remaining habitats were intermediate. Differences in functional richness and divergence were largely driven by the presence of small schooling planktivores in the massive and branching Porites habitats. These results indicate that differential structural complexity among coral communities may act as an environmental filter, affecting the distribution and abundance of associated species traits, particularly those of small-bodied schooling fishes.