Abstract: Ninety-eight SSR markers were used to compare the genetic diversity in 202 Chinese cultivated rice varieties. The result showed a high level genetic diversity in Chinese cultivated rice. All the 98 loci revealed a total of 1350 alleles. The number of allele per locus (Na) ranged from 3 to 39, with an average of 14. The Nei’s genetic diversity index of per locus (He) was 0.733 with a range from 0.125 to 0.955. The polymorphism information content (PIC) varied from 0.122 to 0.953, with a mean of 0.680. Number of rare alleles (the allele frequency < 5%) (Nr) was 913 and genetic richness (Rs) was 8.33. There exited a significant difference in genetic diversity between landrace and modern rice varieties. Landrace (Na=1219, He=0.747, PIC=0.710, Nr=756, Rs=8.50) had more variation than modern rice (Na=919, He=0.704, PIC=0.650, Nr=529, Rs=7.01). Diversity analysis in chromosomes demonstrated that the Chromosome 1 of modern rice had higher genetic diversity than that of landrace. Further analysis showed interval specificity of genetic improvement in the level of whole genome for modern rice.