To study the origin and evolution of Asian cultivated rice (Oryza sativa L.), 98 accessions of Asian cultivated rice and 125 accessions of common wild rice (Oryza rufipogon) were selected for sequencing analysis. Through sequencing the atpA gene, rps16 intron, trnP-rpl33 inter spacer, trnG-trnfM inter spacer and trnT-trnL inter spacer in chloroplast genome in rice, the haplotype network and phylogenetic tree were made with bio-information software. The results showed that the tested common wild rice had more Indels and SNPs than the Asian cultivated rice. Both the haplotype network and phylogenetic tree divided all test materials into three groups. GroupⅠconsisted by accessions from the Japonica subspecies and the common wild rice, Group II included mainly the accessions of Indica subspecies, while Group III were of the accessions of the common wild rice. Importantly, Group II and Group III had a close relationship, which indicated that the Japonica and Indica Subspecies were originated from Japonica-like and Indica-like common wild rice separately, supporting the Double Domestication Hypotheses of Asia cultivated rice. All the materials of common wild rice with a close relationship to Asian cultivated rice were identified to be collected from South China, implicating South China might be the origin center of Asian cultivated rice.