The agamid species Trapelus lessonae (Rastegar Pouyani 2000) is one of the widespread species of the family Agamidae in Iran. It is active in day time and particularly can be seen during first and last hoers of day in summer time. In Iran, it is distributed from northwest towards southeast of the country on the foot hills, open planes and alpines along the Zagros mountain chain. In order to evaluate phylogenetic relationships among different population of this taxon in its range in Iran, several populations of this species were collected within its range from Azerbayejan, Kurdistan, Kermanshah, Hamadan, Ilam, Markazi and Isfehan provinces since mid May to early September 2012. Total genomic DNA was extracted from 33 samples, the mitochondrial gene ND2 were amplified and sequenced in all the specimens. Phylogenetic relationships among different populations were reconstructed using variety of methods (e.g Maximum Parsimony, Maximum Likelihood, Bayesian Inference) and programs (e.g Mega, Mr. Bayes and Paup). The reconstructed phylogeny showed the distinct position of all populations in the tree with relatively high resolution. Considering the branch pattern of the phylogenetic tree and the amounts of genetic distances among populations, it is clear that the populations of Azerbayejan, Kurdistan, Kermanshah and Ilam are closely related and all can be attributed to the same taxon in species level. However, the populations of Isfehan and Hamadan are relatively far from the western populations so that they probably can be considered as a distinct species.