Abstract: To estimate the genetic diversity of common wild rice from the Largest Original Habitat in Guigang, Guangxi and further to distinguish the individuals within the population. Twenty-five SSR loci distributed on the twelve chromosomes of rice were used to study the genetic diversity and structure of 349 wild rice individuals. The results showed that, the mean number of allele (A ) was 6 and the effective number of allele (Ae ) was 2.23. Expected heterozygosity (He ) was 0.44, and observed heterozygosity (Ho ) was 0.40 as well as the Shannon index (I ) was 0.88. The population could be divided into four subsets structure, and more than 90% of individuals could be distinguished. It had abundant genetic diversity within the population and SSR molecular markers was the effective method to distinguish most of individuals in the group also to improve protection efficiency of wild rice.