We examined geographic variations of absolute and relative lower molar sizes (size proportions among M₁, M₂, and M₃) in the Japanese macaque (Macaca fuscata) using skull specimens obtained from 13 locations. We compared the geographic patterns and climatic factors. The size of M₁ significantly and negatively correlated to the annual and coldest month mean temperatures and precipitation for both males and females. The M₂/M₁ and M₃/M₁ scores significantly and positively correlated to the annual and coldest month mean temperatures. The geographic pattern in the size of M₁ was consistent with Bergmann's rule; however, the sizes of M₂ and M₃ did not correlate with temperature, and were not consistent with the rule. The geographic pattern in relative molar sizes (M₂/M₁ and M₃/M₁ scores) indicated that populations living in colder climates possess a larger M₁ in relation to M₂ and M₃. Therefore, the correlations of M₁, M₂/M₁, and M₃/M₁ scores to temperature involve an increase in the size of M₁ in a colder climate. In macaques, the functions of the different molars (M₁, M₂, and M₃) do not differ (they all exhibit grinding function, unlike differentiation between carnassial and other molars in Carnivora), whereas the timing of molar eruption does. In other words, at young ages (1.5–3.5 years), M₁ erupts and is in occlusion, whereas M₂ and M₃ do not erupt and are not used for mastication. Therefore, the geographic pattern in the relative molar sizes may be attributed to increasing survivability in harsh winter climates by increasing occlusal surface in younger animals.