We analyzed the sequence alignment on 25 AA rice and 24 non-AA rice chloroplasts using two length diversity markers (ORF 100 and ORF29-TrnC GCA) and four sequence markers existed in introns of rps16 gene and TrnT U-GU-TrnL UAA spacer to explore the chloroplast diversity of different types of rice using PCR amplification and sequencing. Results showed that in terms of the length of ORF100 and ORF29-TrnC GCA , chloroplast DNA (cp DNA) of Hainan ordinary wild rice, Dongxiang ordinary wild rice, Hepu ordinary wild rice and three-line cytoplasmic male sterile wild rice were indica-type, Chaling ordinary wild rice, Fusui ordinary wild rice, Niwara wild rice, Brazilian upland rice and Lemont were japonica-type among in AA genome. Besides, all non-AA wild rice was japonica-type. There were 4 indica-japonica markers utilizing introns of rps16 gene and TrnT UGU-TrnL UAA. We found that all the ordinary wild rice in Chaling and Fusui of AA genome presented as japonica specific sites, while the others owned two indica and japonica specific sites, respectively. There were two indica-japonica sites separately and a 6-base specific fragment in three-line cytoplasmic male sterile materials except Yuetai A, simultaneously, 2-base difference from Hainan wild rice. Moreover, Brazilian upland rice and Lemont were entire japonica specific sites. Result of three markers indicated that the cp DNA of non-AA wild rice was japonica-type and result of one marker showed indica-type. Sequencing results also suggested that wild rice existed many polymorphic base sites, CCDD genome, wart wild rice and malay wild rice had their own specific sites. In conclusion, significant differentiation trend of indica-japonica exhibits in chloroplast of ordinary wild rice, and non-AA wild rice is generally japonica-type. The cytoplasmic polymorphism level of three-line sterile lines is low.