We studied the reef fish assemblage of eight reefs within the oceanic archipelago of Fernando de Noronha, off northeastern Brazil. In a total of 91 belt transects (20×2 m) we recorded 60 species from 28 families. The 25 most abundant species accounted for about 98% of all fish recorded in this study and most of these species are widely distributed in the Western Atlantic. The majority of fish counted were planktivores (37.0%), followed by mobile invertebrate feeders (28.5%), territorial herbivores (11.3%), roving herbivores (10.5%), omnivores (7.1%), macrocarnivores (6.5%) and sessile invertebrate feeders (0.03%). In terms of biomass, roving herbivores were the most representative (41.8%), followed by mobile invertebrate feeders (19.9%), macrocarnivores (14.3%), omnivores (14.0%), piscivores (8.3%), planktivores (1.4%), territorial herbivores (0.3%), and sessile invertebrate feeders (0.03%). Overall, density and biomass of fishes were positively correlated with coral cover and depth, and negatively correlated with wave exposure. These relationships are probably a response to the habitat complexity provided by the higher coral cover in deeper reefs (>10 m) of the archipelago or to the lower water turbulence below 10 m deep. Carnivores and mobile invertebrate feeders were mainly influenced by depth and non-consolidated substratum, planktivores and omnivores by wave exposure and herbivores by algal cover. Although our results suggest that habitat characteristics may play a role in determining the distribution of some fish species, we also found several habitat generalists, suggesting that the community is dominated by versatile species.