The skate genus Atlantoraja is composed of three species (A. castelnaui, A. cyclophora, and A. platana) which differ from the other Riorajini species, Rioraja agassizii, in regards to their clasper features, squamation and presence of a caudal fin. Despite of being distributed along Southwestern Atlantic and commonly captured by fisheries in Brazil, Uruguay and Argentina, detailed accounts on external and internal morphology are scarce and the taxonomic status of Atlantoraja species was not revised so far. The aim of this study, therefore, is to review the taxonomy of the genus Atlantoraja, updating information on type specimens and clarifying misidentifications among species, and to describe in detail anatomical structures such as neurocranium, visceral arches, pelvic girdle, dermal denticles and teeth. Lectotypes and paralectotypes are designated for Atlantoraja castelnaui and A. cyclophora. Notes on intraspecific variation within species are also provided. Atlantoraja cyclophora and A. platana are more similar to each other than to A. castelnaui in regards to the squamation (body dorsal surface smooth vs. densely covered by prickles) and color pattern of body dorsal surface, position of orbital foramina, overall shape of neucrocranium and body measurements. Lastly, we discuss the morphological differences among species of Atlantoraja and recommend the inclusion of characters presented here in future cladistic analyses.