Finlayson's squirrel (Callosciurus finlaysonii) is distributed in lowland forests in Southeast Asia. The pelage colour is conspicuously polymorphic, and 16 subspecies have been described based on pelage colour patterns. Among them, 12 subspecies are distributed in Thailand, of which 7 are on the mainland and 5 are on islands. In addition, the distribution range of another closely related species, Pallas's squirrel (Callosciurus erythraeus), overlaps the range of C. finlaysonii in western Thailand. In this study, phylogenetic analysis based on mitochondrial DNA suggested that C. finlaysonii and C erythraeus did not form separate monophyletic groups. This C finlaysonii/C. erythraeus complex in Thailand consisted of seven divergent groups, some of which may have arisen from isolation due to large rivers and seas: (1) C f. noxlcinnamomeus, (2) C f finlaysoniilfollettiltrotteri, (3) C. f. menamicus, (4) C erythraeus, (5) C. f. annellatus, (6) C. f. bocourtilboonsongi/floweri, and (7) C. f. frandseni/albivexilli. Pelage colour did not consistently correspond to these genetic groups, suggesting that specific colours may have been acquired multiple times or the genes associated with colour may have variations and polymorphisms within subspecies. Several small populations in the lowlands and on small islands had lower genetic diversity. To conserve the local genetic diversity of C finlaysonii, it may be necessary to enact legal restrictions on their trade and hunting. (C) 2017 Deutsche Gesellschaft fur Saugetierkunde. Published by Elsevier GmbH. All rights reserved.