Abstract: Genetic diversity of 65 japonica rice varieties which were approved by Jiangsu from 2007 to 2013 and 7 control varieties were analyzed by 48 SSR primers. The results indicated that polymorphism existed in the experimental materials, and a total of 101 alleles loci were detected. The average number of alleles per SSR locus was 2.40 with a range from 2 to 4. The average value of gene diversity index was 0.21 with a range from 0.03 to 0.64. The value of polymorphism information content (PIC) was 0.18 with a range from 0.03 to 0.58. The intervarietal genetic similarity coefficient ranged from 0.78 to 0.97, with an average value of 0.91 for 65 japonica rice varieties. The genetic similarity coefficient ranged from 0.87 to 0.97 for 95.4% of the 65 japonica rice varieties. In three types of japonica varieties, genetic diversity of the late-maturation mid-season japonica had the highest number of allele, mean locus PIC value and genetic diversity index were higher than that of late japonica and mid-maturation mid-season japonica. Clustering analysis through UPGMA method showed that 65 japonica rice varieties could be clustered into two groups except ‘Tongjian 981’, ‘Yangnongdao1’ and ‘Yandao 10’. The japonica rice varieties in Jiangsu had close genetic relationship with each other and the genetic diversity was not enough at present. The varieties bred by the same breeding organization had a closer genetic relationship.