Wild rice (Oryza rufipogon) has been recognized as the ancestor of Asian cultivated rice (Oryza sativa). However, where and how cultivated rice originated from wild rice has been debated for a long time in the World. Moreover, whether the two subspecies of the Asian cultivated rice, indica and japonica, were domescated with the ways of single origin or multiple origins is still considerably controversy, and whether they origined in China or aboard is still the focus of debate among international scholars. In this study, we collected 184 accessions of the Asian cultivated rice and 203 accessions of Oryza rufipogon to be sequenced with 5 genes: cox3, cox1, orf224, ssv-39/178, rps2-trnfM in mitochondrial genome of rice Through the study of the gene diversity of the five genes, we verified the following propositions: first, the origin of japonica is in China, and the origin of indica is not only in China but also in foreign countries; second, the subspecies of Asian cultivated rice were domesticated with two origins, in another words, common wild rice exists the indica-like and japonica-like types, and the two subspecies were evoluted from the indica-like wild rice and the japonica-like wild rice respectively.