All extant porpoise species show paedomorphic skeletal traits. These traits are hypothesized to be connected with rapid growth to reproductive size and could thus show geographic variation according to ecological circumstances. To investigate this, skeletal ontogeny was compared among harbour porpoises from California, West Greenland, the inner Danish waters, and the Sea of Azov. Porpoises from California grew to larger sizes than Danish porpoises, which were again larger than Greenlandic porpoises, whereas Azov porpoises were smallest. Size differences were largely attributable to differences in timing of offset of growth. Expression of paedomorphosis followed the same pattern among populations and sexes as adult sizes; Californian porpoises were less paedomorphic than the other populations across all assessed traits, whereas porpoises from Azov were the most paedomorphic. We propose that the larger size and less profound paedomorphism seen in Californian porpoises are attributable to fluctuation of prey availability, owing to variation in upwelling on which productivity in Californian waters depends. Skull shapes after correction for allometry were significantly different among all populations, Sea of Azov porpoises being most divergent. There was no overlap of skull shapes between the Atlantic, the Pacific, and Azov, supporting the current division of harbor porpoises (Phocoena phocoena (L., 1758)) into three subspecies (Phocoena phocoena phocoena (L., 1758), Phocoena phocoena relicta Abel, 1905, and Phocoena phocoena vomerina Gill, 1865).