We studied variation in morphometric and meristic characters and color pattern in the salamander Hynobius kimurae, examining 282 males from 24 localities encompassing the whole distributional range of the species in Honshu, the mainland of Japan. Multivariate analyses of 24 morphometric characters resulted in the separation of two groups, (1) eastern populations from the Kanto District to Shizuoka Prefecture of the Chubu District, and (2) central-western populations from Aichi Prefecture of the Chubu District westwards. Similar groups were recognized in meristic characters and color pattern. These geographic patterns of morphological variation coincided with the pattern of genetic differentiation inferred from allozymes in this species, except for the position of one population from the intermediate region. Some of the morphometric and meristic characters significantly correlated with environmental parameters of sampling sites, and suggested effects of differential habitat conditions among populations on the geographic morphological variation in this species.