Taiwan Island is thought to have formed around 6.0 million years ago, but, the formation of a ‘proto-Taiwan’ began around 9.0 million years ago. During the late Miocene, the proto-Taiwan is thought to have been a part of the Asian mainland. During the Pleistocene, Taiwan Island was again occasionally connected with the Asian mainland. Several mammal species migrated from the Asian mainland to Taiwan during Pleistocene glacial periods. Despite the connections between Taiwan and the Asian mainland, Taiwan has some endemic mammal species. Recent genetic evidence suggests that arboreal squirrels (Petaurista alborufus, P. philippensis, Belomys pearsonii, and Tamiops maritimus) adapted to Taiwan's mountainous forests are endemic species. Since these squirrels may have similarly evolved from separate ancestral stock in Taiwan, we investigated the phylogenetic relationship of Perny's long-nosed squirrel (Dremomys pernyi) from Taiwan and the Asian mainland by using mitochondrial cytochrome b gene sequences. The Taiwanese form was distantly related to the mainland form, showing deep genetic difference (10.18–10.88%). Therefore, D. pernyi could include at least two distinct species, with the Taiwanese form being a species endemic to Taiwan.