In this study, the phenotypic and genetic diversity analysis were conducted in 124 foxtail millet germplasm accessions. The higher variations of qualitative traits, such as seedling leaf posture and spike panicle, and larger variation coefficient on stem weight per plant, individual biomass, and single panicle weight were observed, implying the higher genetic diversity being present in this collection.?The tested materials can be divided to six groups at the genetic distance 7.0 by adopting the phenotype clustering Ward method, and each group represented different characteristics. In addition, The genetic diversity analysis by 52 SSR primer combinations were performed. Fifty-two specific bands were obtained, with the average genetic similarity coefficient of 0.834 and the variation range of 0.615-0.962. These materials were divided into four groups in the genetic similarity coefficient of 0.746. The accessions in groupsⅠand Ⅱwere collected from Hebei, and the genotypes in group Ⅲ were derived from Kazakhstan.87.90% of the 124 accessions were assigned into group IV, but no geographical clustering feature was observed. When the genetic similarity coefficients are 0.843 and 0.870, the germplasm in group IV can be divided into 9 subgroups and 7 sub-subgroups, respectively. Thus, based on the phenotypic and genetic datasets, 12 elite accessions of foxtail millet were identified potentially being use in cultivation in Xinjiang.