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The spotted toad-headed agamas Phrynocephalus guttatus (Reptilia, Agamidae) inhabit different types of deserts on the vast territory, spreading from Kalmykia in Russia to the westernmost parts of China. Phrynocephalus guttatus s.l. actually represents one of the youngest species complexes of Phrynocephalus genus and includes several species and subspecies. The majority of them live in Eastern Kazakhstan, several inhabit Transbalkhash region: P. kuschakewitschi and P. incertus; areas of P. alpherakii and P. melanurus are nearby. The aim of our study was to specify the borders of ranges of P. kuschakewitschii и P. incertus, whether they are distinct or these two forms flow smoothly from one into another and if there is a hybridization. We studied 149 samples of spotted toad-headed agamas and we used fragments of mtDNA genes (668 b.p. of COI for all samples, 291 b.p. of cytb and 705 b.p. of ND4 for selected groups). We reconstructed phylogenetic trees with MrBayes ver. 3.2. The three mtDNA markers gave us different picture. In the COI phylogenetic tree, two Transbalkhash populations separated (Taukum and Kabanbay) and they group with P. versicolor, so here we observe either pseudogen influence or traces of old hybridization event benween P. guttatus s. l. and P. versicolor. According to cytb results these two populations are mixed with P. kuschakewitschii, while according to ND4 data Taukum and Kabanbay again stay sepately. More sequences of mtDNA, research on nuDNA markers are needed to clarify the situation. The research was supported by the Russian Science Foundation RSF, grant No. 19-14-00050.