We analyzed morphological variation in external traits of Apodemus speciosus using 1,799 individuals collected throughout its entire distribution range. Clear geographic patterns were not observed in head and body length. Tail length was greater in the Hokkaido and Tokara-Nakanoshima populations and smaller in the Oki Islands populations. Ear length showed geographic trends within the Honshu populations, being smaller in the eastern populations than the western populations. Hind foot length was longer in Hokkaido, Kyushu, and peripheral island populations compared to the Kinki population. Relative head length was larger in the Tsushima and Tokara-Nakanoshima populations than in the Kinki and Chugoku populations. The frequency of hypothenar pad occurrence on the hind foot was biased in many island populations; individuals with hypothenar pads were dominant in the Kii-Oshima and Oki-Chiburijima populations, but individuals without pads were dominant in the Tsushima and Tokara-Nakanoshima populations. The longer tails found in Hokkaido might be caused by arboreal habitat use in these mice. The presence of a larger hind foot was thought to be obtained independently in each population. Biases in hypothenar pad frequency in island populations could be explained by the random fixation of alleles determining the presence or absence of the hypothenar pad.