Jirds (genus Meriones) are a diverse group of rodents, with a wide distribution range in Iran. Sundevall’s jird (Meriones crassus Sundevall, 1842) is one such species that shows a disjunct distribution, found on the Iranian Plateau and Western Zagros Mountains. Morphological differences observed between these two populations, however, lack quantitative support. Morphological differences between geographical populations of Meriones crassus were analysed and compared with those of the sympatric M. libycus. Similarities in the cranial morphology of these species were found, e.g. in a relatively large and inflated bulla. A two-dimensional geometric morphometric analysis was done on the skull of 275 M. crassus and 220 M. libycus from more than 70 different localities in their distribution range. Results confirm cranial differences between specimens of M. crassus from the Western Zagros and those from Africa and Arabia, mainly at the level of the relative size of the tympanic bulla, that were significantly correlated with the annual rainfall and elevation. Moreover, the study supports the hypothesis that the Western Zagros specimens are both a geographically and phenotypically distinct group compared to the other Iranian M. crassus specimens, suggesting that the former might be a distinct species.