For many years, relationships within Chinese Brassica species and subspecies were the subject of much controversy. Sequences of the chalcone synthase gene (Chs) were used to analyze the evolutionary history of Brassica plants from China. Sequences from Brassica were separated into three well-supported groups in accordance with the A, B, and C genomes. SplitsTree analysis recognized three distinct Brassica groups, and median-joining network analysis recognized three distinct haplotypes of Chs. The estimates of Tajima’s D, Fu and Li’s D, and Fu and Li’s F statistics for the Chs gene between the A-diploid and C-diploid were not significant, while those between the A-polyploid and B-polyploid were significant. The results indicated that (1) Chinese Brassica could be divided into three sections – Pekinensis, Juncea, and Oleracea; (2) both tree and reticulate evolution existed in the evolution of Chinese Brassica; (3) B. rapa var. oleifera, B. nigra, and B. oleracea were the parental donors of the A genome, B genome, and C genome in the allotetraploid, respectively; and (4) the relationship between the A and B genomes was closer than that between the A and C, and B and C genomes in Chinese Brassica. These results shed new light on the knowledge about the phylogeny and evolution of Brassica in China that could account for rich resources of Brassica species.