The taxonomy and phylogeny of the subgenus Mus, the Eurasian lineage of the genus Mus, remain unresolved, even for the house mouse (Mus musculus). While the subgenus is diverse in Asia, few studies cover both its morphology and molecular phylogeny. We re-examined 70 specimens identified as M. cervicolor that were collected from central Nepal in 1968 and 1975 and are currently deposited in the Hokkaido University Natural History Museum. To compare morphological features, we examined skull geometric morphometrics and body coloration, and performed a phylogenetic analysis of the mitochondrial cytochrome b gene sequences of representative specimens. The specimens were most likely either M. booduga or M. musculus. The best morphological characteristics for distinguishing the two species were the nasal length ratio, which was high and low, respectively. Mus booduga was found to inhabit altitudes lower than 1000 m and have light ventral fur, while M. musculus inhabited various altitudes up to 3000 m and had variable fur color depending on the altitude. We also discuss the taxonomic status of the fawn-colored mouse M. cervicolor.