The vast Brazilian coast harbors unique and diverse reef fish communities. Unfortunately, relatively little is known about the impact of fishing on these fish species, and few management or conservation efforts are being made to protect them. Here, we examine the effect of different levels of protection on the composition, abundance, and size structure of reef fish species along a 2500 km portion of the Brazilian coastline, noting in particular the relative abundance of endemics and the effect of protection on these species. Pairwise comparisons of sites with different protection status (more versus less protected) were used to determine the potential responses of reef fishes to the establishment of marine protected areas. Highly targeted species (top predators and large herbivores) were significantly more abundant and larger in size within sites with a higher degree of protection, indicating that they benefit from protection, while lightly fished and unfished species were not. These results are consistent with past work documenting the responses of species to protection. Here, we use our results in particular to suggest strategies and provide expectations for managing and protecting Brazilian reef fisheries. Because this biogeographic province lies entirely within the jurisdiction of a single nation, there may be unique and significant opportunities to effectively manage and conserve these fish species.