To test the effect of geographical isolation by ‘Blakiston's Line’ and the possibility of Bergmann's rule being valid, we comparatively examined the morphology of the crania, mandible and teeth of two subspecies of raccoon dog allopatrically distributed in Japan: Nyctereutes procyonoides albus and Nyctereutes procyonoides viverrinus. The Blakiston's Line is a biogeographic border separating mammalian and avian fauna in Japan, including N. p. albus and N. p. viverrinus. Most skull measurements of N. p. albus were larger than those of N. p. viverrinus, suggesting that the body size of N. p. albus could also be larger than that of N. p. viverrinus. Both subspecies were clearly isolated by Blakiston's Line and followed Bergmann's rule, with skulls of the northern subspecies, N. p. albus, larger than N. p. viverrinus. Premolars and molars of N. p. viverrinus were larger than those of N. p. albus, suggesting that N. p. viverrinus may be more frugivorous. The narrow postorbital constriction associated with development of temporal muscles in N. p. albus suggests this subspecies is more carnivorous.