Glycine tabacina （Labill.） Benth.， a perennial species of the subgenus Glycine， is endemic to Fujian province， China， and was listed as a National Grade Ⅱ Key Protected Wild Plant. Rational population sampling to maximize the preservation of genetic diversity is crucial for germplasm collection of this species. In this study， species-specific SSR markers were employed to analyze both inter-population genetic structures across 13 natural populations and intra-population genetic structures in a single-population. The results show that geographically there were extremely low gene differentiation （F_st=0.056）， high expected heterozygosity （H_e=0.741）， high polymorphism information content （PIC=0.70）， and substantial gene flow （N_m=4.445）； intra-population variation （H_s accounting for 78.0% of the total variation） exceeded inter-population differentiation （D_st accounting for 22.0% of the total variation）. The results of this study clearly support that： although G. tabacina is a self-pollinating plant， its geospatial population genetic variation characteristic resembles that of outcrossing plants， which may be attributed to the species' perennial nature facilitating high genetic heterogeneity and extensive long-distance dispersal enabling high geographical gene flow. The fine-scale spatial genetic structure analysis within the single population （Longhai） with higher-level disturbance revealed that the size range of spatial genetic patches among plants was about 5.0 m. When the sampling size was 20-25 plants， 95% of the population's genetic diversity was captured. Based on the findings of this study， we propose the following strategies for collecting G. tabacina germplasm resources： at the population level， at least 20-25 individual plants should be sampled within a population， with an interval of at least 9-15 m between sampled plants. At the geographical spatial level of populations， since G. tabacina in China is only distributed in a narrow coastal area of Fujian province， it is recommended to collect as many populations as possible.