Genetic variations of seventeen rice germplasms were studied using two SSR markers (RM122 and RM390) linked to the rice bacterial leaf blight (BLB) resistance genes.The average number of allele per locus was 10, with a range of 7 (RM122) to as many as 13 (RM390). The highest level of gene diversity value (0.9135) was observed in loci RM390 and the lowest level of gene diversity value (0.7059) was observed in loci RM122 with a mean diversity of 0.8097. The PIC values ranged from a low of 0.6715 (RM122) to a high of 0.9069 (RM390) and averaged of 0.7892. A dendrogram based on genetic distance using UPGMA, indicates segregation of the 17 rice varieties in six major clusters, BR10 and Binadhan 5, which were single variety formed cluster-1 and cluster-2 respectively.