In order to elucidate the genetic diversity and population structure of superior rice species resources in the three gorges reservoir area, this study used 25 pairs of SSR polymorphism molecular markers to analyze the genetic diversity and population structure of 81 superior rice species resources, which were collected from different geographical sources and types in the three gorges reservoir area. The results showed that the above markers could effectively identify the level of genetic diversity of the tested materials. A total of 56 alleles were detected, and the number of alleles detected at each locus was 2~ 5, with an average of 2.44; The number of effective alleles varied from 1.077 to 2.582, with an average of 1.757; the polymorphism information (PIC) ranged from 0.069 to 0.539, with an average of 0.332; the Shannon index ranged from0. 158 to 1.017, with an average of 0.625; and the Nei's gene diversity index ranged from 0.071 to 0.665, with an average of 0.407. Further analysis showed that the average effective allele number of landrace was higher than that of cultivars, while the average allele number and Shannon index of cultivars were higher than that of landrace. However both of them are very similar in terms of gene diversity index, polymorphic information content and expected heterozygosity. By the cluster analysis, population structure analysis and principal coordinate analysis, the tested materials were roughly assigned to two groups. The regional law of the aggregation of various groups was not obvious, and the clustering relationship of varieties was relatively complex. The results of molecular variance analysis showed that the variation between populations was the same as that between varieties, and the variation between populations and varieties was the source of variation.