Abstract: The experiment was conducted to study the genetic diversity and genetic structure of Gymnocarpos przewalskii with 201 individuals sampled from 7 G.przewalskii populations in Xinjiang by using tart codon targeted(SCoT) markers. The 12 random primers were amplified to 145 loci. The percentage of polymorphic bands, Nei's genetic diversity index and Shannon's information index of species and population leve were 97.24% and 76.45%, 0.2638 and 0.2137, 0.4081 and 0.3316, respectively. These results indicated that the genetic diversity of G.przewalskii was higher, and the genetic diversity of the species level was slightly higher than the population level. The genetic differentiation coefficient was 0.1839, indicating that the genetic variation of G.przewalskii mainly existed in populations, differentiation among populations exists partly. The results of Mantel test showed that there were no significant correlation between geographical distance and genetic distance. The results of principal coordinate analysis(PCoA) and genetic structure analysis were some differences, but basically consistent with each other. Therefore, the present status of genetic diversity and genetic structure of G.przewalskii might be related to its evolutionary history, breeding system, geographical isolation and human disturbance.