We measured metric and scored non-metric characters of 242 harbour porpoise (Phocoena phocoena) skulls from the North and the Baltic Sea and subdivided them into three geographical areas: The German Bight, the outer part or transition area of the Baltic Sea (Skagerrak, Kattegat, Belt Seas, Øresund, Kiel Bight, Lübeck Bight, and Fehmarn Belt Sea), and the central Baltic Sea (Arkona Sea and waters off the eastern Swedish coast). A comparison of the skull characters by means of ANOVA, Discriminant Analysis and X2-tests revealed significant differences between the porpoises of all three areas. The results of this study indicate the existence of populations in the Baltic different from the North Sea populations. Further, we found differences between the animals from the transition area and the central Baltic Sea respectively, indicating the occurrence of a separate population in the Baltic proper. We offer a non-migratory scenario as an explanation for the central Baltic stock of the harbour porpoise based on a review of hydrographical conditions and prey species availability.