To identify the house mice collected in Pokhara and Lumbini of Nepal at the subspecies level, morphological and molecular analyses were carried out. Morphologically, two populations collected in Pokhara and Lumbini were distinguished by fur colour, but there was no significant difference in external measurements (p > .05). The phylogenetic analysis results revealed that the haplotypes sequences of mitochondrial DNA (mtDNA) Cytochrome B (CytB) gene distinguished into two distinct clades on a phylogenetic tree representing two subspecies, Mus musculus bactrianus and M. m. castaneus in Pokhara and Lumbini, respectively. In Nepal, the subspecies M. m. bactrianus was not reported before this study. These findings concluded that at least two subspecies, M. m. bactrianus and M. m. castaneus currently exist in Nepal. We estimated that these two subspecies could have introduced together with human migration, while further study is required to understand their evolutionary history and current distribution.
Keywords: CytB; M. m. bactrianus; M. m. castaneus; Nepal; subspecies.