Chinese wild soybean is the direct progenitor of cultivated soybean, having a self-pollinating reproduction system with a low outcrossing rate. This feature would make wild soybean have higher and lower amounts of genetic variation within and between geographical spaces or lower and higher amounts of genetic variation within and between populations. However, sometimes there are higher and lower amounts of genetic variation within and between populations, which may be caused by the stronger gene flow over the effects from environmental stresses, disturbance, and genetic drift or associated with the historical gene dispersal. Gene flow in the wild soybean is closely related to geographical distance. Chinese wild soybean has 4 clear genetic categories: small-seeded (100-seed weight under 2.0 g), medium-seeded (100-seed weight of 2.01–2.5 g), large-seeded (100-seed weight of 2.51–3.0 g) and semi-wild(100-seed weight over 3.0 g) types. The genetic differentiation between typical wild and semi-wild types is the main factor within the species. The genetic boundary of G. gracilis is at the range of 2.51–3.0 g 100-seed weight of Glicine soja, and therefore the classification of G. gracilis as over 3.0 g 100-seed weight against typical wild soybean is reasonable. Some medium-seeded plants and the majority of the large-seeded ones likely have originated from the segregation of hybrid progenies between wild and cultivated soybeans.