This study investigates the reef fish community structure of the world’s smallest remote tropical island, the St Peter and St Paul’s Archipelago, in the equatorial Atlantic. The interplay between isolation, high endemism and low species richness makes the St Peter and St Paul’s Archipelago ecologically simpler than larger and highly connected shelf reef systems, making it an important natural laboratory for ecology and biogeography, particularly with respect to the effects of abiotic and biotic factors, and the functional organisation of such a depauperate community. Boosted regression trees were used to associate density, biomass and diversity of reef fishes with six abiotic and biotic variables, considering the community both as a whole and segregated into seven trophic groups. Depth was the most important explanatory variable across all models, although the direction of its effect varied with the type of response variable. Fish density peaked at intermediate depths, whereas biomass and biodiversity were respectively positively and negatively correlated with depth. Topographic complexity and wave exposure were less important in explaining variance within the fish community than depth. No effects of the predictor biotic variables were detected. Finally, we notice that most functional groups are represented by very few species, highlighting potential vulnerability to disturbances.