The mice of genus Mus are small-size mammals which belong to the family Muridae of the mammalian order Rodentia. Considerable efforts have been devoted to establish the phylogeny of the Mus genus. But it has been difficult to establish clear taxonomy of the Mus genus by traditional morphometric tools due to the existence of subtle morphological differences among different forms. Thus, 17 different systematics studies of Mus genus are in great conflict. Despite the fact that Pakistan encompasses an important part of range of many Mus species, mice populations in Pakistan have not been the subject of any genetic and biogeographic studies. So, there exist some serious ambiguities with respect to the occurrence of Mus spp. in Pakistan. Thus, present study was conducted to find out which species are actually present in the study area Pothwar. True taxonomic status was examined by using molecular markers of Cytochrome b and Mitochondrial control region. The genetic diversity depicted by Maximum likelihood phylogeny and Median joining network revealed three species i.e. Mus musculus, Mus terricolor and Mus cookii, three sub species of Mus musculus i.e. M. m. musculus, M. m. domesticus and M. m. castaneus and four sub lineages of M. m. castaneus. M. m. castaneus proved to be the most abundant and thus most important taxa identified from Pothwar region. M. m. castaneus population in Pothwar proved to be highly diverse on the basis of haplotype and nucleotide diversity indices. Neutrality tests were implemented to study the recent demographic history of each sub lineage. Tajima’s D test suggested recent population expansion in all lineages. The taxa identified by genetic analysis were subjected to morphometric analysis involving body and cranial measurements, description of pelage and characteristics of the molar teeth. Discriminant function analysis (DFA) of morphological, cranial and coat colour variables was executed to predict membership of each specimen to the respective species or lineage identified on the basis of molecular analysis. Resul ts of molecular and morphometric analysis were well concordant in the case of three Mus species as significant morphological segregation was evident at species level. While morphological segregation was not complete between sub-species of Mus musculus and among sub-lineages of M. m. castaneus as DFA showed 50- 70% morphological isolation between these sub-lineages identified by molocular 18 analyses. Chi-square test was applied to test the homogeneity of the distribution of Mus fauna. According to which no habitat wise segregation was evident for genetically identified Mus taxa. This study tried to provide validated information about the genetic identity of Mus fauna of Pothwar. As members of genus Mus are major agricultural pests, this study provides basic information about the distribution and species composition of Mus in Pakistan for developing effective and environment friendly management programs for inhibiting different Mus populations.