ABSTRACT Tropical marine habitats are among the most biodiverse on Earth but are facing accelerated local and global threats. Well-planned marine protected areas (MPAs) are a countermeasure for biodiversity loss and an alternative to maintain ecosystem services and their sustainable uses. Despite the need to improve the ecological representativeness of the Brazilian system of MPAs, basic information on spatial patterns of species distribution and richness is still lacking for several regions. The Abrolhos Region and Vitoria-Trindade Seamount Chain (Abrolhos Seascape) are among the biologically richest marine areas in the Southern Atlantic, and expanding the protection of key habitats in this region can aid Brazil to achieve its national and international conservation goals. This study updated the habitat map and the potential distribution of 546 species of fishes, invertebrates, cetaceans, seabirds, and sea turtles, and identified biodiversity hotspots in the Abrolhos Seascape. Habitat classes were defined based on the probability of occurrence and a comprehensive updated database. Potential species occurrence models and the weighted endemism method, with additional weight to the threatened species, were combined to identify biodiversity hotspots. Our results indicate that although some habitats (e.g. shallow reefs, mangroves, estuaries, and deep ocean), are relatively well represented in the current MPAs, a large portion of habitats with high biodiversity and concentration of endemic and threatened species (e.g. rhodolith beds, mesophotic reefs, slopes and sinkholes), have very low or no representativeness in the current MPAs. Our analysis provides important insights for future conservation planning exercises and highlights the urgent need to effectively protect high biodiverse marine habitats, not only to conserve biodiversity, but also to maintain key ecosystem services in the Abrolhos Seascape.