This article focuses on the five major controversial issues regarding the origin of semi-wild soybeans. Based on our research experience over the past two decades and the expertise in studies of wild (G. soja) vs. semi-wild soybeans, we make an overview on the morphological evidence for the natural hybridization-origin of semi-wild soybean (big-seeded type) and the origin of some rare characters that were found in wild soybean. The results gained from the morphological and molecular evidences supported three grams in 100-seed weight as the cutoff of semi-wild soybean (G. gracilis). The abundant phenotypic variations were observed in wild soybean accessions that represent 2.5g-3.0g in 100-seed weight. By capturing the phenotypic variations of parental lines and derived hybridization progenies as well as the segregation ratios at each of traits, the origin of semi-wild soybean has been confirmed to result from natural hybridization between wild and cultivated soybeans. Meanwhile, our works have indicated that rare characters such as white flower, coloured seed coats (yellow, green and brown), no-seed-bloom, grey pubescence have been introgressed from cultivated soybean to its wild ancestor through the natural hybridization.