Most studies of cetacean habitat use do not consider the influence of anthropogenic activities. We investigated the influence of environmental and anthropogenic variables on habitat use by humpback Megaptera novaeangliae and Bryde’s whales Balaenoptera brydei off the coast of the Brazilian city of Rio de Janeiro. Although there are 2 marine protected areas (MPAs) in this area, few data are available on cetacean habitat use or on the overlap of different cetacean species within these MPAs. Our aim was to evaluate the effectiveness of the MPAs and propose a buffer zone to better protect the biodiversity of the study area. We conducted systematic surveys and developed spatial eigenvector generalized linear models to characterize habitat use by the species in the study area. Habitat use by humpback whales was influenced only by depth, whereas for Bryde’s whales there was the additional influence of anthropogenic variables. For Bryde’s whales, which use the area for feeding, sea surface temperature and the distance to anchorages had a major influence on habitat use. We also showed that neither of the MPAs in the study area adequately protects the hotspots of either whale species. Most of the humpback whale grid cells with high sighting predictions were located within 2 km of the MPAs, while areas of high sighting prediction of Bryde’s whales were located up to 5 km from the MPAs, closer to beaches. Our findings provide important insights for the delimitation of protected areas and zoning of the MPAs.
