A geometric morphometric approach was employed to test a number of hypotheses regarding population structure of the harbour porpoise in the greater Baltic region. Porpoise skulls from Denmark, Sweden, Finland, Germany and Poland were measured with a suite of three-dimensional landmarks. Statistical analyses revealed highly significant shape differences between porpoises from the North Sea, Belt Sea and the inner Baltic Sea. A comparison of the directionalities of the shape vectors between these units found differences that cannot be attributed to a general, continual shape trend going from the North Sea to the inner Baltic Sea. The directionalities of the vectors indicate a morphological adaptation to the specific sub-areas. E.g., in the Belt Sea porpoises, there may be a greater reliance on benthic and demersal prey. Such adaptation may be a result of the topographic peculiarities of the area with variable topography and shallow waters. While the present results show that isolation by distance alone is an unlikely explanation for the differences found within the greater Baltic region, we cannot estimate the level of genetic isolation between areas from morphology.