【Objective】To explore the information of development and differentiation of special micro-environment of wild soybean for sampling wild soybean.【Method】A total of 41 simple sequence repeat (SSR) markers scattered on the whole genome were used to analyze the genetic diversity and genetic structure, and to evaluate the relationship between genetic diversity and spatial distribution of the 16 wild soybean populations with a sample of 612 individuals around Daguanling in Xintian County, Hunan Province.【Result and conclusion】A total of 414 alleles were detected with 41 SSR marks among 612 accessions, and the average number of allelic variations per locus was 10.1, ranging from 4 to 19. The average Shannon’s information index (I) per locus was 1.751 with a range of 0.283-2.542. It was discovered that the region from Xiangxiling to Sangzi had a higher genetic diversity and more allelic variations than other regions, and also had a higher gene flow than the other populations by comparing genetic diversity index of different populations. The wild soybean accessions could be divided into 19 sub-groups by the analysis of population structure with software Structure 2.3 based on mixed model. The populations near the region from Xiangxiling to Sangzi were divided into different sub-groups and the populations far from Daguanling were clustered into different groups separately. There was a positive correlation between genetic distance and geographic distance under the condition that the sample’s distance was less than 1 400 m. The region from Xiangxiling to Sangzi was a diversity center of wild soybean in Daguanling region. Populations near the region apparently had the character of spatial distribution. Genetic diversity was positively correlated with geographic distance and altitude. The population of wild soybean in Daguanling disperse from high altitude to low altitude. The spread model of this region is distance model and continent island model.