Patterns of evolution can be biased by patterns of variability (propensity to vary). However, the effects of variability on evolution at the geographic and inter-subspecies levels have not been investigated extensively. Variation between different populations is the result of evolution. Individual variation within a single population can be indicative of species variability. Therefore, comparing patterns of variation within and between populations can reveal the effects of variability on evolution. In this study, I used two-dimensional geometric morphometric methods to evaluate variation in the shape of raccoon dog skulls within and between wild populations in Japan. In three of the populations observed, the dominant individual variation was cranial tilting. Cranial tilting is also a major variation between Japanese populations that has no correlation with climatic factors. However, differences in another morphological trait involving the frontal bone, parietal bone, and zygomatic arch dominated the variation between the Hokkaido population and other populations in Japan that are often considered to be a different subspecies. This morphological trait was correlated to snowfall. In conclusion, at the intra-subspecies level, morphological evolution in the skull is neutrally driven by variability. However, at the inter-subspecies level, adaptation may have a relatively larger effect on morphological evolution.