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The Persian Jird, Meriones persicus, is distributed from Eastern Anatolia to Afghanistan and western Pakistan. Six subspecies were described based on skull features and coat colours, but the validity of these subspecies is uncertain, and no molecular work has ever been conducted on this species. Iran appears to be a key geographical region in which to revise the systematic and evolutionary history of this species, because five of the six subspecies are present in this country. To evaluate the phylogeographical history and taxonomy of this species in Iran, we used a combination of genetic (cytochrome b gene sequences of 70 specimens) and geometric morphometric (2D landmarks on the ventral side of skull of 258 specimens) analyses. We also used ecological niche modelling to make inferences about the evolutionary history of these lineages. Our molecular data highlight the existence of four genetic lineages, but they only partly correspond to the previously described subspecies. Our molecular and morphometric data confirm the validity of M.p.rossicus and show that it has a wider geographical range than previously thought. M.p.gurganensis and M.p.baptistae are genetically very close. The skull of M.p.gurganensis is morphologically distinguishable from other subspecies. The subspecies M.p.persicus and M.p. baptistae are genetically distinct, but morphologically close. Meriones p.ambrosius is genetically close to M.p.persicus, and additional analyses with more specimens are needed to validate its subspecific status. The genetic structure observed in Iran seems to fit the topography and biogeography of the country and emphasize the role of the Abarkooh, Central and Lut deserts as barriers to gene flow. All intraspecific divergent events within the Persian Jird occurred during the last 1.4My, suggesting that climatic changes probably trigger diversification within this species. Our genetic and species niche modelling results suggest that potential refugial areas persisted during glacial periods for this species in north-western Zagros Mountains, north-eastern Alborz Mountains and Kohrud Mountains.