Abstract: The aims are to clarify the indica- japonica differentiation and the genetic variation of Shanlan upland rice varieties from Hainan. In this study, 34 indica- japonica special InDel markers and 24 SSR molecular markers were used in 22 Shanlan upland rice varieties from Hainan to analyze the characteristics of indica-japonica differentiation and genetic variation. Results of InDel molecular markers showed that, gene frequency variation ofjaponica types ranged from 0.68 to 0.83. Thejaponica -type varieties were the main type, which accounted for 63.6%, whileindica and partialindica were not found. The analysis of altitude gradient showed that, the distribution ofjaponica varieties of Shanlan upland rice in Hainan was more extensive and more adaptable. Genetic variation analysis showed that, 191 alleles were detected in the test varieties, including 86 rare alleles (gene frequency≤0.05), which accounted for 45.03% of the total alleles. The richest genetic diversity of upland rice was found in Qiongzhong County of the three testing areas.