An integrative approach is crucial in discrimination of species, especially for taxa that are difficult to identify based on morphological characters. In this study, we combine genetics and morphology to assess the diversity of Pterasteridae, a sea star family diversified in deep-sea and polar environments. Because of their derived anatomy and the frequent loss of characters during preservation, Pterasteridae are a suitable case for an integrative study. The molecular identification of 191 specimens (mostly from the Southern Ocean) suggests 26–33 species in three genera (Diplopteraster, Hymenaster and Pteraster), which match the morphological identification in 54–62% of cases. The mismatches are either different molecular units that are morphologically indistinguishable (e.g. Pteraster stellifer units 2 and 4) or, conversely, nominal species that are genetically identical (e.g. Hymenaster coccinatus/densus/praecoquis). Several species are shared between the Northern and Southern Hemispheres (e.g. Pteraster jordani/affinis). In conclusion, the taxonomic status of some groups is confirmed, but for others we find the need to re-evaluate the taxonomy at both genus and species levels. This work significantly increases the DNA barcode library of the Southern Ocean species and merges taxonomic information into an identification key that could become a baseline for future studies (pterasteridae-so.identificationkey.org).