Reef fish community structures at three sites in the state of Rio de Janeiro (Pedra Vermelha (PV), Cabo Frio Island—Arraial do Cabo; Mãe Island (MI), Itaipu—Niterói; Comprida Island (CI), Cagarras Archipelago—Rio de Janeiro) were investigated to assess differences in fish species composition, density and distribution of trophic groups, between sites, correlating the observed patterns of fish distribution with environmental factors. Thirty-six visual strip-transects yielded 67 species of 34 families. Studied locations shared at least 40% of all species, mostly of western Atlantic distribution. The three sites presented significant differences on diversity, density and species dominance. CI presented the highest values, except for total density, which was higher at PV, probably due to its partial degree of protection. MI showed the lowest values, suggesting possible impacts from the proximity to the shore. The main trophic categories were omnivores followed by mobile invertebrate feeders, in similarity to what was previously observed for south-eastern Brazil. Inherent habitat features of each location regarding depth, declivity, visibility and rugosity resulted in different species distribution and dominance patterns.