Abstract: The study was designed to characterize the genetic diversity in a set of rice genotypes with different adaptation to saline soil using microsatellite markers (SSR markers). For this analysis a total of 50 SSR primers across the 12 chromosomes were taken up out of these 50 primers, 37 primers were polymorphic. The average number of alleles per locus was 5.69, indicating greater magnitude of diversity among the plant materials. The average PIC value 0.732 conformed the markers used were highly informative. The cluster analysis grouped the 27 genotypes into nine clusters. Cluster I consisted of nine varieties and all are indica type. Cluster II consisted of three varieties all are salt tolerance. Cluster III consisted of two rice varieties these are tolerant to drought. Cluster IV consisted of seven varieties, which are high yielding varieties. Cluster V consisted of CR1009, which is high yielding variety. Cluster VI consisted of Pokkali and CSR23 both are highly tolerant to salinity. Cluster VII, VIII and IX are mono-clusters consisted of CSR27, CSR10 and Jeeragasamba. The maximum similarity value of 0.786 was observed between the varieties of IR36 and IR64 indicated that these were more closely related. The minimum similarity value of 0.237 was observed between the genotypes IR36 and CSR10 indicated that these two varieties were highly divergent. The varieties possessing high genetic distance value could be utilized for the development of high yielding varieties than the highly closed varieties.