Social voles of the genus Microtus consist of at least eight nominal species occurring in the Western Palearctic. Despite the significant influence of Middle Eastern Geo-climatic heterogeneity on small mammal diversification, this area remains largely unexplored. In this study, we considered mitochondrial cytochrome b phylogeny and chromosomal data to assess taxonomy and intraspecific variability within two closely related social voles, Microtus irani and Microtus schidlovskii in the Middle East. We also performed univariate and multivariate analyses to elucidate the craniodental variations between the studied voles. We confirmed the close relationship of the “irani-schidlovskii” complex while providing pieces of evidence for their distinct species’ status. In addition, our new material from Iran outlines a novel view on the distribution of the taxonomically obscure Iranian vole M. irani with an undescribed subspecies from Chahar-Mahal & Bakhtiari Province in southwestern Iran.