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. In Brazil, there is a need to improve the ecological representativeness of the national system of MPAs by incorporating poorly protected ecosystems. 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 help Brazil to achieve its national and international conservation goals. This study updated the habitat map and the potential distribution of 632 species of fishes, invertebrates, cetaceans, seabirds, and sea turtles, and identified priority areas for biodiversity conservation in the Abrolhos Seascape. Habitat classes were defined based on the probability of occurrence and a comprehensive updated database. Models for species distribution and the weighted endemism method, with additional weight to the threatened species, were combined to identify priority areas for biodiversity conservation. Our results indicate that although some habitats (e.g. shallow reefs, mangroves, estuaries, and deep ocean), are relatively well represented, a large portion of habitats identified as priority areas for biodiversity conservation (e.g. rhodolith beds, mesophotic reefs, shelf slopes and sinkholes), have very low or no representativeness in the current MPAs. Urgent action is needed to effectively protect these habitats, not only to conserve biodiversity, but also to maintain key ecosystem services in the region.