Abstract: According to the distribution of Phrynocephalus vlangalii hongyuanensis in Zoige Wetland，three geographic units: Zoige Xiaman (XM)，Hongyuan (HY)，both in Sichuan Province and Maqu (MQ) in Gansu Province were defined. We used molecular methods to reveal these unit’s genetic variation and diversity. A 785bp fragment of the mtDNA ND4-tRNA^leu was determined from 72 samp1es in seven populations of P. vlangalii hongyuanensis. Seven variable nucleotide sites and nine haplotypes were identified in the 785bp fragments. As a whole，the haplotype diversity was high (0.806±0.024)，but the nucleotide diversity was low (0.00231±0.00016). In a single population，MQa，MQb and XMb had very low genetic diversities，and XMc had a much higher one. The Kimura 2-parameter distances among all the populations were small (0.001-0.005)，and the distance between MQa and XMa was the greatest. Analysis of molecular variance (AMOVA) showed that the three units were distinctly different (P<0.01)，and 62.61% of the total genetic diversity was attributable to variation among units. There were 3 haplotypes shared among XM and HY，and no geographic clustering was observed except MQ from the TCS network. The results from the mismatch distribution analysis and Fu’s Fs test (Fs=－2.21937) implied that there might be a recent population expansion in the XM unit，and this may be the reason why XM had a high haplotype diversity but a low nucleotide diversity. We estimate that the MQ and XMb have lower diversities because of some very recent geographic events，such as the formation of the Yellow river’s upriver and the Zoige Wetland. Although they are distinctly different，not enough time has passed for them to have diverged a great genetic distance.