Skates are frequently caught as by-catch during commercial longline fishing operations within CCAMLR subareas 48.3 and 48.4. Morphological evaluations of the by-catch in these subareas indicate that up to three species from the skate genus Amblyraja occur: A. georgiana, A. georgiana sp. anon and Amblyraja taaf. In this report, we present results from the first population genetic analysis of these Amblyraja skates to assess if their current morphological classification during by-catch assessment reflects potential genetic discontinuities. Our results reveal that it is sampling location (geography), rather than morphology, that is the major determinant of population differentiation in these Southern Ocean skates.