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The five-toed jerboas of the genus Allactaga inhabit arid areas of Asia and North Africa and are widely distributed in deserts, semideserts, and steppe regions of Iran. Many morphological and morphometric studies have been carried out on this genus; however, there is little molecular data available on them. Therefore, their phylogenetic relationships need to be evaluated. Here, using sequences of 903 and 632 bp of two mitochondrial DNA genes, cytochrome b (Cytb) and cytochrome oxidase subunit I (Cox1), the phylogenetic relationships of five nominal species of Allactaga were evaluated from the Iranian Plateau. Phylogenetic trees were constructed on the basis of maximum parsimony, maximum likelihood, and Bayesian analyses. The resulting trees supported seven major clades: (1) Allactaga firouzi and A. hotsoni, (2) A. williamsi, (3) A. euphratica, (4) A. elater from Esfahan and Tehran, (5) A. toussi, (6) A. elater from Golestan, and (7) A. elater from Kashmar and Golestan. On the basis of the results of current study, A. firouzi and A. hotsoni are synonymized, while A. elater could be considered a complex species with three subclades. In addition, the geographic distribution analysis of the species was clarified and as a result, A. euphratica is a new record for the Ilam region.