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We provide a diversity assessment of the agamid genus Phrynocephalus Kaup, 1825. We analyze COI mtDNA barcodes from 385 individuals sampled all over Phrynocephalus range. We apply the ABGD, ASAP, bGMYC, mlPTP and hsPTP species delimitation algorithms to analyze the COI gene fragment variation and assess the species diversity in Phrynocephalus. Nine species groups are revealed in Phrynocephalus in agreement with earlier studies on the phylogenetic relationships of the genus. We demonstrate that the present taxonomy likely underestimates the actual diversity of the genus. Alternative species delimitation algorithms provide a confusingly wide range of possible number of Phrynocephalus species—from 54 to 103 MOTUs (molecular operational taxonomic units). The ASAP species delimitation scheme recognizing 63 MOTUs likely most closely fits the currently recognized taxonomic framework of Phrynocephalus. We also report on 13 previously unknown Phrynocephalus lineages as unverified candidate species. We demonstrate that the ASAP and the ABGD algorithms likely most closely reflect the actual diversity of Phrynocephalus, while the mlPTP and hsPTP largely overestimate it. We argue that species delimitation in these lizards based exclusively on mtDNA markers is insufficient, and call for further integrative taxonomic studies joining the data from morphology, mtDNA and nuDNA markers to fully stabilize the taxonomy of Phrynocephalus lizards. [ABSTRACT FROM AUTHOR]