Methods of species delineation have recently received renewed interest. Following recently outlined protocols, I test species boundaries in toad-headed lizards of the 'Phrynocephalus przewalskii' complex. MtDNA gene trees revealed four mitochondrial clades that correspond to the geographic distributions of traditionally identified 'P. frontalis, P. przeswalskii ' and 'P. versicolor'. Principal Component Analyses of metric and meristic traits were able to successfully differentiate ' P. frontalis' and 'P. przewalskii', but only in allopatric populations. Mantel tests reveal that metric morphology shows a significant association with mtDNA haplotypes. Congruence between mtDNA and morphological variation supports the presence of two species: 'P. frontalis' and 'P. przewalskii'. Intermediate morphology in individuals from sympatric populations of these lineages indicates hybridization in contact zones. Pliocene and Pleistocene glaciations played a large role in the evolutionary history of this group, followed by range expansion that brought these lineages into secondary contact and eventual hybridization.