Geographic variation of the sizes of lower molar (M₁ size) and relative lower molar sizes (size proportions among M₁, M₂, and M3) were examined in two species of closely related Japanese field mice (Apodemus speciosus and Apodemus argenteus). To determine the cause of the geographic variations observed, phylogeographic structure, interspecific competition, climate, and location (mainland or island) were compared. With regard to the phylogeographic structure, the sizes of the molar and the relative molar sizes in A. speciosus did not differ between two major clades (mainland vs. Hokkaido and peripheral islands), whereas the phylogeographic structure was not examined in A. argenteus, as no clear phylogeographic structure was evident. The sizes of M₁ and relative molar size (M₃/M₁ score) in A. speciosus differed significantly between the mainland and islands; however, there was no significant difference between islands within and outside the distribution of A. argenteus. Interspecific competition between the two species may thus not be considerable. Climatic factors (temperature) and relative molar sizes (M₂/M₁ and M₃/M₁ scores) were significantly correlated in the mainland populations of A. speciosus, indicating that geographic variations in relative molar sizes may be affected by climate. In addition, M₃/M₁ scores varied more in the islands than on the mainland, suggesting effects of genetic drift. However, M₁ size increases in the island populations of the two species are not attributed to the climate, but are explained by the so-called Island Rule. Geographic variation in A. speciosus is thus likely attributable to various effects.