Deeper reefs are often considered to be less susceptible to local and global disturbances, such as overfishing, pollution and climate change, compared to shallow reefs and therefore could act as refugia for shallow water species. Hence, the interest on deeper reefs has happened at a time when shallow reefs are undergoing unprecedented changes. Here we investigated the hypothesis that fish community differed from shallow to deeper reefs due to factors apart from habitat structure and quality and therefore discuss for the first-time insights of a "deep refuge hypothesis" from Brazilian reefs. We collected data on fish community, benthic community and physiological conditions of two coral species on shallow (< 6 m) and deep reefs (> 25 m). No significant difference on substratum composition was observed comparing sites and depths. Additionally, physiological data on corals also showed similar oxidative status and growth conditions when comparing the two-coral species in shallow and deep reefs. Conversely, our study demonstrated strong differences on reef fish communities in terms of abundance, species richness, trophic groups, size classes and groups of interest when comparing shallow and deeper reefs. Fish abundance was 2-fold higher and species richness was up to 70% higher on deeper reefs. Also, a significant difference was observed comparing trophic groups of reef fish. Macrocarnivore, Mobile invertebrate feeders, Planktivores, Sessile Invertebrates Feeders and Roving Herbivores were more abundant on deeper reefs. On the other hand, Territorialist Herbivores almost exclusively dominated shallow reefs. Strong differences were also observed comparing the abundance of reef fish groups of interest and their respective size classes between shallow and deeper reefs. Ornamental, Great Herbivores and Groupers showed clear differences, with higher abundances being observed in deeper reefs. Considering size classes, larger individuals (> 15 cm) of Great Herbivores, Groupers and Snapper were uniquely recorded at deeper reefs. Additionally, individuals with > 30 cm were recorded almost exclusively on deeper reefs for all the analyzed groups of interest. Our findings suggest that fishing pressure on the target species may be attenuated on deeper reefs, and these regions may therefore be considered as areas of refuge from shallow water impacts. Therefore, the likely potential for deeper reefs protect species from natural or anthropogenic disturbances increases the attention of marine conservation planning and resource management on including deeper reefs in protected areas.