We described the morphological types, genetic variation and structure in Chinese wild soybean genetic resources. We found that not only did the evolutionary bottleneck occur in the domestication of cultivated soybean from wild soybean, but also the differentiation bottleneck appeared between the different phenotypes of the same characters. Here we also introduced our most recent studies answering about some long-term questions over whether there is genetic differentiation among strains of different seed sizes within wild soybean species, where the genetic boundary between the typical wild and semi-wild types lies, how semi-wild soybean was originated, which side the semi-wild soybean is taxonomically closer to between the wild or the cultivated soybean, whether there are genetic differences between the smaller (3-4 g 100-seed weight) and the outsize (over 8.5g) seed-sizes of semi-wild soybean, whether there is genetic differentiation between large-seeded semi-wild soybeans and less-evolved primitive soybean landraces, whether the outsize semi-wild soybeans (over 8.5g 100-seed weight) belong to the cultivar, which of seed size and seed-coat colour is more important in the evolutionary degree in wild soybean and whether cultivated soybean genes have introgressed into the wild soybean. We think that the true transitional-intermediate ancestors have disappeared during the domestication of cultivated soybeans, and some genes as such controlling white flower, grey pubescence, and no-seed bloom introgressed from the cultivated into wild soybeans.