Top predators have a strong influence on the structure and dynamics of marine ecosystems. These organisms have been largely used as indicators of the effectiveness of marine protected areas (MPAs). In Brazil, the impact of fisheries on reef species, such as groupers and sea basses, and the importance of local marine reserves in the maintenance of these fish communities are still poorly understood. Here we assessed the assemblage of groupers and sea basses (Epinephelidae and Serranidae) inside and outside the Arvoredo Marine Reserve (AR), a MPA in Santa Catarina State, southern Brazil. Density and biomass of 13 fish species (7 Epinephelidae and 6 Serranidae) were recorded. The most abundant groupers were Epinephelus marginatus and Mycteroperca acutirostris, while Serranus flaviventris and S. balwini were the most abundant sea basses. Grouper biomass was significantly higher inside the reserve, indicating the effectiveness of this MPA for target and threatened species, such as E. marginatus. In contrast, biomass of sea basses was higher outside the MPA, as a possible result of prey release effect. Despite the higher biomass of groupers inside AR, spearfishing records from the 1960s indicate that there is still a long way to a full recovery of the biomass of top predators, especially groupers and sharks. Thus, a more effective enforcement and longer-term protection are necessary to restore fish stocks and ecosystem health in these reefs.