Present study aimed to address molecular diversities of the small five-toed jerboa Allactaga elater Lichtenstein, 1825, and the Toussi jerboa Allactaga toussi Darvish et al., 2008, in marginal geographic distribution of the genus in Iran. The study involved 35 individuals of A. elater and A. toussi, from the east and central parts of Iranian plateau. The two probabilistic phylogenetic algorithms, Maximum Likelihood (ML) and Bayesian Inference (BI), applied on 68 sequences of the two mitochondrial genes (34 cytochrome b and 34 cytochrome c oxidase subunit 1), retrieved reciprocal monophyly of the two species. Independent species status of A. elater and A. toussi is further evident from their sympatry in eastern Iran. Each of these species was further subdivided into two deeply divergent phylogeographic lineages within Iranian plateau, showing high level of genetic divergence ranging from 7-10.7 % for cytb and 7.8-12.4 % for cox1 genes. Such values exceed the intraspecific level of variation in rodents.

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