Abstract The morphology of the skull contains considerable ecological information about a species, because the skull contains sensory organs that are used to look for food, compete for mates, or to migrate. Spotted seals ( Phoca largha ) and harbor seals ( Phoca vitulina ) are similar in body size and pelage color but differ in habitat use and reproductive biology. The current study aims to clarify differences in the shapes of skulls in the spotted and harbor seals using geometric morphometrics and to discuss whether ecological differences can explain morphological differences in skulls. First, we discovered that the age at which the shape of skulls stopped changing was 7 years in both species, using the linear‐threshold model. Using a total of 75 landmarks, 54 individuals (25 spotted seals, 29 harbor seals) that were older than the age at which skulls stopped changing were correctly identified at a rate of 100%. The total of 75 landmarks was narrowed down to eight key landmarks that resulted in an identification accuracy rate of 100% using random forests. Of the eight landmarks, seven were related to feeding apparatus, indicated that the harbor seal had a broader mouth and mandible than the spotted seal. Because of both species were dietary generalists and classified as pierce feeders, we suggested that the different features in the shapes of their skulls were caused not only by differences in their feeding behavior but also other differences related to reproductive behavior.