Soybean (Glycine max (L.) Merrill) germplasm in Southern China is extremely diverse. In order to explore the differentiation and evolution among geographic sowing-seasonal ecotypes of the Southern China Soybean Germplasm Population (SCSGP), we tested a sample set of accessions comprising 359 of the spring-sowing (SP) ecotype and 341 of the summer–autumn-sowing (SA) ecotype for their flowering date and sensitivity to seasonal photo-thermal changes in Nanning, Guangxi, China. The sample set and another 175 wild annual accessions were genotyped with 60 representative simple sequence repeat (SSR) markers. The SCSGP is characterised by its geographic differentiation (four geo-regional ecotypes), especially its sowing-seasonal differentiation (SA and SP ecotypes), and their combinations (eight geo-seasonal eco-populations). The ecological differentiation coincided with genetic differentiation in terms of allele richness and genetic distance. Neighbour-joining clustering among accessions by using SSRs indicated SA varieties to be the primitive ecotype relative to SP. The SA ecotype of Eco-region III (SA-III) was the most primitive among the eight geo-seasonal eco-populations, from which evolved SA-IV, and then SA-VI and SA-V. The SP ecotype was mainly evolved from its older SA counterpart, starting from SP-III emerging from SA-III accompanied by its introduction to Eco-region IV and other boarder regions. The evolutionary relationship among the geo-seasonal eco-populations was validated further with the analysis of multi-population specific-present alleles, which supports the hypothesis of Southern China origin of cultivated soybeans.