21 SSR primers were used to assess the genetic diversity of 62 common wild rice individuals from Zhangpu County Fujian Province, Hainan Province. Results indicate that common wild rice in Zhangpu County Fujian Province has a high level of genetic diversity: 74 alleles were detected from 21 loci , A= 3.5238, Ae=2.0629, He =0.4635, Ho=0.2465, I= 0.7918; t estimated by the fixation index(F=0.4304) is 0.3982, it is suggested that the mating system of common wild rice in Zhangpu County Fujian Province is a type of cross-pollinate system with a high self-breeding rate; For degree of differentiation, Shitanhu population is higher than that of Gutang population.