The ecological and conservation status of the geographically isolated Black Sea harbour porpoise is currently unknown. Although it has been suggested that Black Sea harbour porpoises are distinct from other populations, the implementation of specific conservation plans has been hindered by the absence of a genetic and morphological study with large sample sizes. We sought to test the hypothesis that Black Sea porpoises differ from those in the Atlantic Ocean using cranial morphology and mitochondrial DNA variation. A total of 177 adult skulls from the Atlantic coast of France, Danish North Sea including Skagerrak and Inner Danish Waters, Greenland and the Black Sea were scored for 22 morphological variables. A portion of the mitochondrial control region was sequenced for 146 ind. from the eastern north Atlantic, the northern Aegean Sea, the Sea of Marmara and the Black Sea. Within the Black Sea, we found relatively low levels of genetic diversity, and no statistically significant differentiation. However, the Black Sea population shares no haplotypes with the eastern Atlantic populations, suggesting that they have been separated for thousands of years. Black Sea porpoises also show significant morphological differences from other populations, with smaller body and skull size, wider and longer rostrum, smaller orbital length, smaller internal nares and condylar widths and larger occipital ridge. Our results demonstrate that harbour porpoises from the Black Sea, Sea of Marmara and the northern Aegean Sea (eastern region): (1) are genetically differentiated; (2) have been reproductively isolated for a considerable period of time; and (3) are likely to be on an independent evolutionary pathway. We recommend that harbour porpoises from the eastern region be recognized as the subspecies Phocoena phocoena relicta.