In this study, 14 accessions of upland rice (Oryza sativa L.) named Shanlan Rice by Li Ethnic people, 69 accessions of Asian cultivated rice (Oryza sativa L.) and 120 accessions of common wild rice (Oryza rufipogon) were selected for sequencing analysis to study the origin and evolution of upland rice in Li Ethnic communities in Hainan Province of China. Five high mutation regions of SSⅡgene, ITS gene and Ehd1 gene from nucleus genome, the ndhc-trnv inter spacer from chloroplast genome and cox3 gene from mitochondrial genome in rice were chosen to be sequenced. The results showed that the gene diversity of Shanlan rice was the lowest while the common wild rice was the highest and that of Asian cultivated rice was in the middle. 85 percent of Shanlan Upland Rice was japonica. In addition, Shanlan rice had a close genetic relationship with common wild rice from Guangdong, and Hunan province but not Hainan Province, which inferred that Shanlan rice may be originated from common wild rice from Guangdong, and Hunan province.