Environmental factors play an important role in the evolution and genetic variation of species. To clarify the relationship between genetic diversity and environmental factors of Gazella subgutturosa in Xinjiang, in this study the mitochondrial DNA cytochrome b gene (1140 bp) and control region (1100 bp) sequences of Gazella subgutturosa were analysed from 84 individuals in 11 populations from across the species’natural range within Xinjiang by using PCR and direct sequencing methods. The results showed that the Gazella subgutturosa population in Xinjiang seems to show high haplotype but low nucleotide diversity, these results indicated that the Gazella subgutturosa investigated in this study exhibited low levels of genetic diversity. The results revealed by the analysis of correlation between environmental factors and the genetic diversity of various groups showed that altitude, annual precipitation, annual temperature, population are the main environmental factors affecting the genetic diversity of Gazella subgutturosa in Xinjiang, among which altitude is the key environmental factor. Our results provide a theoretical basis for effective protection and management of Gazella subguttrosa in Xinjiang.