To. test for isolation by mountain ranges in small arboreal mammals, phylogeography of Pallas's squirrel .Callosciurus erythraeus) was investigated using complete mitochondrial control region sequences (1,079–1,081 bases). This common species is distributed in the low and middle elevations of Taiwan, Republic of China. We examined 71 specimens from 6 sites in 3 study regions divided by mountain ranges in Taiwan. The 43 haplotypes found in the Taiwan populations revealed association with geography. There were 4 main mitochondrial DNA phylogroups (northern, western, southern, and eastern), but 4 haplotypes were not included in any phylogroup. Distribution range of each phylogroup was similar to defined geological categories, suggesting mountain range isolation influenced populations of C. erythraeus. The 4 phylogroups may be the result of glacial refugia during the Pleistocene.