Abstract: In order to evaluate the genetic diversity of the wild soybean (Glycine soja) in different regions of Shaanxi Province, the genetic diversity and genetic structure among 6 natural populations of wild soybean and 1 population of cultivated soybean (Glycine max) were analyzed by molecular markers of SSR. 113 alleles were detected in 13 microsatellite loci; the mean number of alleles per locus (A) was 8.69; the effective number of alleles per locus (N_e) was 5.632; the mean expected heterozygosity (H_e) was 0.482; and the mean observed heterozygosity per locus (H_o) was 0.080. The Shannon diversity index (I) was 0.657, with the proportion of genetic differentiation among populations (F_ST) as 46.5%. The research shows that the genetic diversity of wild soybean has a higher level in Shaanxi Province. The genetic diversity of wild soybean is generally higher than that of cultivated soybean. Along with the altitude increasing, the genetic diversity of wild soybean variation is declining. The wild soybean germplasm resource is rich in central and southern Shaanxi Province, and the population has high genetic diversity, therefore, it is speculated that the region is the center of genetic diversity of wild soybean in Shaanxi Province.