Morphometric differentiation among six strains of musk shrews (Suncus murinus) originating in Bangladesh (BAN), Sri Lanka (SRI), and four Japanese areas, Nagasaki (NAG), Okinawa Island (OKI), Tokunoshima Island (TKU), and Taramajima Island (TR), was examined by use of skull and external measurements. These data were compared with mitochondrial DNA (mtDNA) differentiation previously reported. Significant sexual dimorphism was observed in all morphometric characters of the six strains, except for two characters in the TR strain. The six strains were clearly grouped by principal component analysis into three body-size types: large BAN shrews, intermediate SRI shrews, and small Japanese shrews. By canonical discriminant analysis, the NAG strain was further distinct from the other three Japanese strains despite their apparent similarities in external morphology, and was characterized by having the most unusual shape in the six strains. No individuals were misclassified as to their geographic origin for both sexes of the six strains. The morphometric differentiation pattern based on only the first canonical variate, extracting an overall size factor, was concordant with the mtDNA differentiation pattern (rss = 0.944, P < 0.001 in males and rss = 0.930, P < 0.001 in females). In contrast, the morphometric differentiation pattern estimated from the second to the fifth canonical variates, representing shape factors, was apparently discordant with the mtDNA differentiation pattern (rss = 0.467, P > 0.05 in both sexes). It was previously reported that a partial premating reproductive isolation mechanism is caused by the difference in body size between mating pairs. Thus, body size may be a factor useful for understanding the mechanisms of population differentiation in this species.