Individual variations in skull and lower carnassial morphology within a wild population of raccoon dog were examined using geometric morphometric techniques. We compared individual morphological variations by using relative warp analysis, and then tested morphological integration between the skull and carnassial by using partial least square (PLS) analysis. The most marked variation in skull shape was the dorsoventral flexion; i.e., deformation from klinorhynchy to airorhynchy. Two remarkable variations were observed, including tilting between the trigonid (or carnassial blade) and the talonid in the lower carnassial, and the relative sizes of the trigonid and the talonid. This observed variation in skull shape was similar to previous reports of variations among dog breeds that correlate with a polymorphism of the Runx2 gene. This polymorphism has also been reported to correlate with snout length, which is strongly related to carnivorous or omnivorous dietary adaptations, across the entire order Carnivora. Our results in the lower carnassial were also similar to previously reported patterns observed for carnivorous or omnivorous dietary adaptations among Carnivora. However, in our PLS analysis between skull and carnassial shapes, we only found a significant correlation in a lower dimension, suggesting a lower degree of integration. These results indicate that shape variations, which could be sources of natural selection in the skull and carnassial, were present in a wild population, suggesting high evolvability of these variations in the raccoon dog and the order Carnivora in general.