Morphological variation was examined in large Japanese field mice, Apodemus speciosus, of five populations from the Izu Islands (from Oshima, Shikinejima, Niijima, Kozushima and Miyakejima), four from the Oki Islands (from Dogo, Nishinoshima, Nakanoshima and Chiburijima), and four from the Japanese mainland of Honshu. Univariate and multivariate (PCA) analyses were conducted on the basis of body-, mandible-, and molar-measurements. Overall, the insular mice had a tendency toward gigantism, and also showed marked morphological differentiation among the islands. The sizes of the mandible and molar were inversely correlated to island area and temperature, thus suggesting a selective effect. Although faunal diversity might be related to the morphological variation in size, there was no clear relationship between the morphological variation and biotic factors such as predation and competition. The populations from the Izu Islands underwent marked morphological divergence, suggesting founder effects. The Izu Island are oceanic and have probably never been connected with Honshu, hence mice were likely transported from Honshu. On the other hand, the Oki Islands had been connected with Honshu in the late Pleistocene. The founders of the insular mice related to the history of the islands could have likely affected the morphological variation.