Abstract: The genus Tripterygium is an immune suppressor in the Chinese traditional medicines. Due to the habitat destruction and anthropogenic over-exploitation, the wild genus Tripterygium plants have decreased dramatically in recent years or even been endangered. It is critical to evaluate and protect genus Tripterygium wild resource. In this research, simple sequence repeat (SSR) molecular markers were applied to the investigation of the genetic diversity and genetic structure of 28 populations for genus Tripterygium (396 samples from 9 provinces in China). We found a high level of genetic diversity (percentage of polymorphic loci PPL=77.29%, Shannon's information index I=0.639 4; Nei's expected heterozygosity H=0.359 9) and high genetic differentiation among the populations (gene flow N_m=0.228 7). Based on Nei's genetic distance, the phylogenic tree of populations was constructed and 28 populations were divided into 6 clusters according to STRUCTURE clustering analysis. T. hypoglaucumwas was mainly divided into 3 clusters, including Sichuan, Yunnan and GuizhouChongqing. T. regelii was separated to cluster 4, while T. wilfordii was divided into two clusters:the transition type LQ and NY were divided into cluster 5, and the others were in cluster 6. These results provide a theory basis for the conservation of wild resource, research of genetic polymorphism and molecular marker for assisted breeding of genus Tripterygium.