Clione limacina (Phipps, 1774) was attained from a broad bipolar distribution in latitudes of 40°N and 40°S. So far southern populations have been described as a subspecies and even a separate species based on morphological and physiological characters. In this study we found a 23.17% (± 0.59%) difference in cytochrome c oxidase subunit I (COI) gene sequences between C. limacina collected from the Arctic and Antarctic oceans. Our work indicates that Clione limacina from the Southern and Northern Hemisphere are not genetically similar enough to represent a single bipolar species and confirms their separate taxonomic status on molecular level.