Genus Allactaga, also known as the jerboa, is represented by 3 cryptic species as A. williamsi, A. elater and A. euphratica in Turkey. Although the relationships among these species were identified morphologically, the validity of the species and sub-species of this genus have not been precisely clarified by molecular data. The aim of the present study is to survey the genetic structure and the validity of Allactaga populations distributed in Turkey inferred from 1049 bp of the mitochondrial DNA cytochrome b (Cytb) gene and 430 bp of 12SrRNA. Bayesian tree and the median-joining method reveal the existence of 3 species of Allactaga in Turkey. Divergence time analysis prove the speciation of the genus Allactaga was in the Pleistocene, namely A. euphratica was most like A. williamsi, supported by fossil molar measurements. On the other hand, sub-species of A. williamsi (A. w. shmidti, A. w. laticeps, A. w. williamsi) are not clear and are connected to the same node. Also, A. w. shmidti grouped both A. w. williamsi and A. w. laticeps. Thus the validity of shmidti has become problematic and might be denied.