Divergence patterns among some Callosciurus squirrel species are affected by geographic isolation by Southeast Asia’s huge rivers. Currently, divergence by rivers is found within C. prevostii, occurring widely in Sundaland. Therefore, there may be similar biogeographical effects on Callosciurus species sympatric with C. prevostii. To test this hypothesis, we examined phylogeographical characteristics of C. notatus based on mitochondrial cytochrome b gene sequences. This squirrel is widely distributed from the Malay Peninsula to Sumatra, Borneo, Java, and adjacent small islands. It has many synonyms and subspecies. We collected specimens from the Malay Peninsula, Sumatra, and Borneo. Interestingly, specimens from Sumatra did not show monophyly, with one very closely related to specimens from Borneo. Specimens from the Malay Peninsula had diverged from the others. This phylogeographical pattern was different from that of C. prevostii reported previously and cannot be explained by geographical isolation from ocean or rivers. In addition to examining more specimens from many parts of Sundaland, future studies should consider the complicated effects of ocean, rivers, and other geographical structures on the phylogeography of this species.