Morphological differentiation in skull shape in small toothed whales is sometimes explained as driven by differences in ontogeny or adaptation to a benthic or pelagic habitat. To test these hypotheses, the comparison was made, using two-dimensional geometric morphometry, between neighbouring populations of harbour porpoises from the north-eastern Black Sea and the adjoining Sea of Azov, from the same genetically isolated subspecies, both known for their extreme paedomorphosis in body and skull development but differing in seasonal habitats (very shallow waters vs open sea). There were major differences between populations in the following traits: in Azov animals, rostrum was slightly shorter and more deflected downwards; premaxillary eminences shifted backward and facial region proportionally longer; more concave facial fossa and higher vertex; lower, downward-facing foramen magnum. Meanwhile, each of the populations followed its own ontogenetic trajectory. Therefore, differences in skull shape between populations were primarily directed by habitat. Shape differences were less discriminating than size; they might involve both echolocation and feeding mechanisms and could be associated with suction feeding. These adaptations were characterized by mixed allometric patterns including both paedomorphosis and peramorphosis in their ontogeny. Shallow habitat was found to be critical in forming specific adaptations even for animals migrating between different habitat types.