Ecosystem functioning is structured by species’ ecological traits within an ecosystem. As such, metrics quantifying variation in the traits of populations (i.e. functional diversity) can outperform traditional taxonomic metrics in predicting ecosystem functioning. In response to mounting anthropogenic disturbances, preserving ecosystem functioning is a foremost concern. However, the extent to which protected areas assist populations and ecosystems to retain functionality in the face of recurring disturbances remains largely unknown. This study used Lady Elliot Island, Eastern Australia, to determine how coral cover and coral traits are linked to the functional diversity of coral reef fishes in a protected area. We surveyed reef flat fishes using a stereo-DOVS (diver operated video system), and corals were sampled using benthic photo quadrats. Fishes and corals were divided into functional groups using traits describing their ecology, morphology and physiology. Coral cover and functional diversity were linked to the functional diversity of coral reef fishes. These results indicate the importance of coral cover and functional diversity, as greater benthic diversity provides more niches to enhance coral reef fish functional diversity. Enhancing coral reef fish functional diversity, and therefore coral functional diversity, is fundamental in conferring resilience against disturbances as well as preserving ecosystem functioning.