Evolutionary history of Callosciurus squirrel species seems affected by geographical isolation by huge rivers in Southeast Asia. Geographical isolation by rivers may have influenced phylogeographical structure between and within Callosciurus species. In Sundaland, Southeast Asia, however, phylogeographical structure within Callosciurus species may be explained by geographical isolation among islands. In a test of the effects of rivers and islands, we examined phylogeographical characteristics of C. prevostii based on mitochondrial cytochrome b gene sequences. This squirrel is distributed from peninsular Thailand to Sumatra and Borneo and adjacent small islands. We collected specimens from four geographically different populations (the Malay Peninsula, central Sumatra, eastern Sumatra, and Borneo) and conducted phylogeographical analyses. Interestingly, the two Sumatra populations, geographically separated by the Batang Hari River, the longest river in Sumatra, did not show monophyly: the central Sumatra population was closely related to the Malay Peninsula population. The specimen from Borneo had clearly diverged from the others. Present geographical isolation by the ocean does not completely explain the phylogeographical structure of this species. The riverine barrier hypothesis helped explain their evolutionary history. Future studies should examine more C. prevostii specimens from more different places in Sundaland.