To evaluate and quantify sexual dimorphism of skull shape and assess the ontogenetic background for differences, samples of 134 harbor porpoise (Phocoena phocoena) and 85 Dall's porpoise (Phocoenoides dalli) were compared in terms of cranial shape and shape ontogeny using three-dimensional geometric morphometrics. After correction for allometry, no sexual differences were detected in harbor porpoise, while Dall's porpoise showed statistically significant sexual dimorphism of skull shape. Since no sex-specific differences were detected in the directionalities of the ontogenetic vectors, we cannot reject that the dimorphism is innate. Based on the different mating systems of the two species and the lack of sexual dimorphism in the harbor porpoise, the dimorphism in Dall's porpoise is most likely a result of sexual selection in relation physical competition for mates given that male skulls provide room for larger neck muscles with a more favorable lever arm.