To examine the origin of Callosciurus erythraeus introduced to Japan, we compared mitochondrial DNA control region sequences of eight haplotypes from Japan with those of 42 haplotypes from Taiwan. There were two distinct phylogroups in Japan. Six haplotypes from Japan were included in the Taiwan population, suggesting that they could have been introduced from Taiwan. Two haplotypes, however, were distantly related to the cluster consisting of all Taiwanese haplotypes and six Japanese haplotypes. The uncorrected genetic distances (5.2–5.7%) between these two haplotypes and the out-group (Callosciurus finlaysonii from Laos) were less than those (8.3–9.8%) between these two haplotypes and the cluster consisting of the other six Japanese haplotypes and all Taiwanese haplotypes. Both C. erythraeus and C. finlaysonii have variable external characteristics, such as pelage color, and include many variable subspecific forms, so that it is difficult to evidently identify both species on the basis of their external characteristics. Callosciurus finlaysonii may have been also introduced in Japan with both species now coexisting in Japan.