Abstract: Phrynocephalus przewalskii is one kind of lizards inhabiting inclusively in the desert that has controversial viewpoints on its phylogeny. Based on mitochondrial ND2 gene of 119 samples from 12 geographic populations, we analyzed the effects of environmental factors on the variation of genetic diversity, as well as its relationship to P. versicolor. The results showed that these populations clustered into three major lineages, with P.versicolor embedded within one lineage. The twelve populations had great genetic diversity variation, which was tightly linked with local altitude, annual precipitation, and variation of annual precipitation. High latitudes, increased annual precipitation and great variation in annual precipitations may all have resulted in the decrease of genetic diversity. It thus assumed that altitude can change the genetic diversity of different geographic populations of P. przewalskii resulting from the effects of different local annual precipitation.