Abstract: Shanxi province of China acts as one of the main producing areas of common millets and also a center of local varieties and farmer germplasm resources. Exploration of genetic diversity in common millet germplasms will provide a scientific basis for studying the origin and evolution of proso millet, which would strengthen gene transfer between varieties of common millet and facilitate the utilization of excellent resources. In this study, we analyzed the genetic differences among 57 common millet accessions from Shanxi province by 27 pairs of SSR polymorphic primers. The statistical analysis were conducted by software PowerMarker 3.25, PopGen 1.32, MEGA 5.0, Structure 2.3.4 and Ntsys2.11. Within this collection, 71 alleles were detected with an average of 2.6296 alleles at each locus. The number of effective allele account for 76.94% of the observed one. The Shannon index of all primers ranged from 0.4140 to 1.0446, with an average of 0.7686, The range of PIC was 0.0601-0.7158, with an average of 0.5667. The values of genetic diversity indexes such as the observed heterozygosity have no much difference between two ecotopes. Basing on Neighbor-joined genetic distance, 57 materials were divided into 3 groups, the group Ⅰ belongs to the Loess Plateau spring & summer-sowing ecotopes, the group Ⅱ belongs to the Loess Plateau spring & summer-sowing and Northeast spring-sowing, the same as the group Ⅲ. The analysis of genetic structure divided 57 common millet accessions into three groups. In terms of the values of Shannon''s information index and PIC, the green group is higher than of the blue and red. The results of two cluster analysis are consistent and they showed a close correlation between geographical region and the method of clustering. Meanwhile the materials in northern of Shanxi province were distinguished from the middle and the southern of Shanxi province by the means of PCA, The result indicated that the genetic background of two ecotopes has obvious differences due to geographical and climatic factors, which is consistent with the result of genetic structure analysis between populations. Thus, the genetic diversity of common millet resources in Shanxi province was abundant.