To provide a genetic basis for japonica rice breeding,the genetic similarity and cluster of 139 accessions of improved japonica rice varieties from 12 provinces and cities of China were analyzed using 34 SSR markers.Totally 198 alleles were detected among these improved japonica rice varieties with the average number of alleles per pair of primers was 5.3235.RM320,RM531,RM1,RM286,and RM336 showed more alleles,which were 15,12,11,9,and 9,respectively.RM320,RM336,RM286 and RM531 showed higher genetic diversity indexes,which were 2.3324,2.0292,1.8996,and 1.7820,respectively.The range of genetic similar index among improved japonica rice varieties from different provinces was from 0.321 to 0.914,with the average of 0.686.There was a high genetic similarity among improved japonica rice varieties from Heilongjiang,Jilin,Liaoning,Ningxia,and Yunnan,which were located in similar latitude or similar ecological environment,while there was a low genetic similarity between improved japonica rice varieties from Guizhou and Jiangsu,and other provinces which were located in more different latitudes and ecological environments.The markers of RM320,RM531,RM1,RM286,and RM336 fit to be used in analysis of genetic diversity for improved japonica rice variety.The genetic similarity among improved japonica rice varieties from different provinces was closely associated with genetic basis of parents,and was also correlated with latitude and ecological environment where the varieties were bred. To provide a genetic basis for japonica rice breeding, the genetic similarity and cluster of 139 accessions of improved japonica rice varieties from 12 provinces and cities of China were analyzed using 34 SSR markers. Lowest 198 alleles were detected among these improved japonica rice varieties with the average number of alleles per pair of primers was 5.3235.RM320, RM531, RM1, RM286, and RM336 showed more alleles, which were 15,12,11,9, and 9, respectively. RM320, RM336, RM286 and RM531 showed higher genetic diversity indexes, which were 2.3324, 2.0292, 1.8996, and 1.7820, respectively. The range of genetic similar indexes among improved japonica rice varieties from different provinces was from 0.321 to 0.914, with the average of 0.686. There was a high genetic similarity among advanced japonica rice varieties from Heilongjiang, Jilin, Liaoning, Ningxia, and Yunnan, which were located in similar latitude or similar ecological environment, while there was a low genetic similarity between improved japonica rice v arieties from Guizhou and Jiangsu, and other provinces which were located in more different latitudes and ecological environments. The markers of RM320, RM531, RM1, RM286, and RM336 fit to be used in analysis of genetic diversity for improved japonica rice variety. genetic similarity among improved japonica rice varieties from different provinces was closely associated with genetic basis of parents, and was also correlated with latitude and ecological environment where the varieties were bred.