Multivariate morphometric analysis of 31 cranial and dental characters was applied to a sample of 141 adult specimens of mice from southern and south-eastern Asia, and sub-Saharan Africa. The material under study represented five species of two subgenera, viz., Asian Mus (M. terricolor [= M. dunni], M. caroli, M. cervicolor) and African Nannomys (M. minutoides, M. setulosus). The results were largely congruent with molecular data based on various markers. The two subgenera were found to be morphologically clearly differentiated from each other, as were also Mus (Nannomys) minutoides and M. (N.) setulosus. Within the subgenus Mus, the morphometric distance of M. terricolor, a member of the so-called “Leggada” group, from other species was also high. On the contrary, M. cervicolor and M. caroli appeared to be similar to each other morphologically. In M. cervicolor, no substantial morphometric differences were found between two subspecies, M. c. cervicolor and M. c. popaeus. The patterns of morphological differentiation between respective samples did not fully reflect geographical distribution in M. (N.) minutoides and M. (N.) setulosus.