The Ching Hai Toad-headed Agama (Phrynocephalus vlangalii) complex is a small toad-headed viviparous lizard that is endemic to the Qinghai-Tibetan Plateau.A fragment of mtDNA ND4-tRNALEU from 189 samples in 26 populations was used to infer the phylogeographic history of this species complex in the upper reaches of the Yellow River.Phylogenetic analyses revealed that P.vlangalii and another proposed species (P.putjatia) do not form a monophyletic mtDNA clade,which in contrast with a previous study,includes P.theobaldi and P forsythii.Lineage diversification occurred in the Middle Pleistocene for P.vlangali (ca.0.95 Ma) and in the Early Pleistocene for P.putjatia (ca.1.78 Ma).The uplift of the A'nyemaqen Mountains and glaciations since the mid-late Pleistocene,especially during the Kunlun Glaciation,are considered to have promoted the allopartric divergence of P vlangalii.The diversification of P.putjatia may be triggered by the tectonic movement in the Huangshui River valley during the C phase of Qingzang Movement.Subsequently,the glacial climate throughout the Pleistocene may have continuedto impede the gene flow of P.putjatia,eventually resulting in the genetic divergence of P.putjatia in the allopatric regions.Demographic estimates revealed weak population expansion in one lineage of P vlangalii (A2,the Qaidam Basin lineage) and one lineage of P.putjatia (B2,the north Qinghai Lake lineage) after approximately 42 000 years before present.However,constant population size through time was inferred for two lineages (A1 and B1),the source of Yellow River lineage of P.vlangalii and the southeast of Qinghai Lake lineage of P putjatia,possibly due to stable populations persisting in areas unaffected by glacial advances.Our results also suggest:1) at least four differentiated lineages of P.vlangalii complex may have evolved allopatrically in different regions during the Pleistocene glaciation events; 2) in support of several recent studies,P.putjatia is a valid species,having a more wide distribution than previously considered; and 3) a hypothesis referring to P.v.hongyuanensis,inhabiting in the source region of the Yellow River,being synonymous with P v.pylozwi is supported.