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Mesalina watsonana is a well‐known species of small lacertid lizards with an extensive species distribution that exhibits high genetic diversity. The species has a wide distribution range in Iran, some parts of Turkmenistan, Afghanistan, Pakistan, and northwest India. This study aims to generate phylogenetic and phylogeographic evidence to derive taxonomic recommendations supporting. Furthermore, this species can be used as a model for examining Iranian Platuea's historical biogeography. We conducted a very detailed sampling of its distribution and used genetic approaches. Phylogenetic analyses were done implementing two mitochondrial (Cytb and 16S) and one nuclear (C‐mos) gene fragments. Combination of these results indicated that seven well‐supported distinct clades exist within this species complex, i.e. Kerman clade, Esfarayen clade, Halil clade, Ardestan clade, M. watsonana clade, Bardaskan Clade, and Khuzestan Clade in Iran. Also, our results revealed that several distinct clades diverged due to geologic events when the Dasht‐e‐Kavir and the Zagros Mountains were formed. It seems that the ancestor of M. watsonana spread to Iranian Plateau before the formation of the Zagros Mountains. Orogenic activities of the Zagros Mountains and the formation of deserts have influenced the separation of these lineages from the Late Miocene by allopatric speciation. Generally, our findings suggest that each of the seven clades corresponding to distinct geographic regions deserves to be elevated to the species level. [ABSTRACT FROM AUTHOR]