Abstract: A 838 bp fragment of mtDNA ND4-tRNA^Leu gene was sequenced for 66 individuals from five populations (DB: Dabancheng, TU: Turpan, SS: Shanshan, HL: Liushuquan, HD: East district of Hami) of Phrynocephalus axillaris distributed in east of Xinjiang Uygur Autonomous Region. Seventeen haplotypes were identified from 29 nucleotide polymorphic sites in the aligned 838 bp sequence. Excluding DB, there were relatively high haplotype diversity (0.600±0.113) ≤ h ≤0（.922±0.012) and low nucleotide diversity (0.00082±0.00020) ≤ π≤（0.00917±0.00037) in the whole and the rest four populations. The result of phylogenetic analysis showed that the haplotypes from five populations formed cladeⅠ(DB+TU+SS) and cladeⅡ (HL+HD). Network analysis further revealed the phylogeographical structure of these five populations. Analysis of molecular variance (AMOVA) indicated that the significant genetic divergence (81.67%, P<0.01) existed among populations, which was not obviously correlated with the geographic distances between populations inferred from isolation-with-distance analysis (r=0.5324, P=0.1196). The demography analysis implied that TU and HL might have experienced the recent population expansion; SS and HD might be relatively stable. With extremely low genetic diversity, DB might be influenced by the special environment and be experiencing the bottleneck effect. It followed that the significant genetic differentiation among the five populations of P. axillaris might be the consequence of habitat changes resulting from the geological events and climate oscillation since Pleistocene and genetic drift.