The geographical variations of the skulls were osteometrically examined in the gray-bellied squirrel (Callosciurus caniceps) from the populations of Korat, Ranong, southernmost Thailand, and Terutau Island. The skull size was larger in northern population than in the southern population in the continental mainland. The zoogeographical influences of the Isthmus of Kra remained unclear, since the plots from Korat population were intermingled with those from southernmost Thailand population in the principal component charts. Although Korat population has been thought to belong to north group, we suggest that Ranong and southernmost Thailand populations may contain individuals from both north and south groups separated by the ancient Kra barrier. Terutau Island population was similar to southernmost Thailand population in skull size, although Terutau population has been isolated in the island and separated from the south group of the Isthmus of Kra. In the proportional analysis the interorbital space was narrower and the binocular sense has been well-developed in Terutau population. It suggests that this population has been highly adapted to arboreal behavior. In contrast, the skull with larger interorbital space was more adaptive for terrestrial life in Korat population. The canonical discriminant analysis could clearly separate the four populations in the scattergrams of discriminant scores.