Two species of field mice, Apodemus argenteus and A. speciosus, occur in sympatry across the Japanese archipelago. The inter- and intraspecific patterns of morphological differentiation have been evaluated, using a Fourier analysis of the mandible outline. The relative importance of the effect of insular isolation and latitudinal climatic gradient on the size and shape of the two species was assessed by a comparison of the populations from the large island of Honshu and the surrounding small-island populations. The size variation in A. argenteus is correlated with the climatic gradient whilst the shape variation corresponds mainly to a random differentiation of the small-island populations from a Honshu-like basic morphological pattern. A. speciosus displays increased size on small islands, and its shape variation is related to both the climatic gradient and insularity. Finally, the two species are differentiated by both the size and shape of the mandible across the Japanese archipelago, suggesting that interspecific competition between both species is reduced via niche partitioning. Our results emphasize the importance of insular isolation on shape differentiation, but a part of the morphological differentiation is also related to the latitudinal climatic gradient. Isolation on small islands could have favoured such a response to environmental factors by lowering the gene flow that prevents almost any significant differentiation within Honshu populations.