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Here we provide the results of ancestral area reconstruction for two species complexes of Phrynocephalus genus. Species complex Ph. helioscopus (including Ph. persicus) inhabits takyr deserts in a wide area from Astrakhan region in Russia to Ily river valley in China. Ph. guttatus species complex is also widespread in this territory, but inhabits different type of deserts, from sandy dunes to solid gravel deserts. We analysed sequences of: a) COI gene and b) a dataset of 4 concatenated mtDNA genes (COI, cytb, ND2, ND4), all obtained during our previous projects. COI alignment comprised 75 sequences for Ph. helioscopus s.l. and 84 sequences Ph. guttatus s.l. The concatenated alignment included 36 sequences from different Phrynocephalus species. To reconstruct the ancestral areas of these two species complexes, we analysed the concatenated dataset using Lagrange. For phylogeographic reconstructions, we used BEAST 1.7.5 for COI alignment only, using Brownian diffusion and LRRW models of continuous phylogeography. The results were visualised in SPREAD and Google-Earth.The Lagrange analysis results suggest two regions of Ph. helioscopus s.l. diversification — Turan and/or the Middle East. The more sensitive continuous phylogeographical analysis under LRRW model suggests Iran as an ancestral region, which seems to be the most appropriate ancestral region. According to Lagrange analysis, there are also two possible ancestral regions for Ph. guttatus s. l.: Middle Asia and/or Central Asia. Continuous phylogeography analysis in BEAST using Brownian diffusion model supports the Middle Asia scenario, while LRRW model resulted in a logic error.Our results are in agreement with other studies. Ananjeva N.B. and Tuniev B.S. (1992) suggested Iranian Plateau as the possible area of Ph. helioscopus complex diversification. The split within the complex and the following expansion was likely caused by the uprise of Iranian Plateau. High diversity in the south-eastern part of the area allows us to suggest it as the second center of diversification within Ph. helioscopus sensu stricto (Solovyeva et al., 2011). Our analyses place this center near Navoi in Uzbekistan. According to Dunayev E.N. (2009), Ph. guttatus and Ph. versicolor separated near the border of modern Dzhungaria and East Kazakhstan, arid conditions existed there before Miocene(Chkhikvadze et al., 1983). Ph. guttatus expanded into Middle Asian deserts, with several groups dispersing farther to the West and even reaching the northern part of Turan region (Ph. g. moltschanowi and Ph. g. salsatus). These hypotheses are also in agreement with our results.