Genetic diversity is pre-requisite for any crop improvement program as it helps in the development of superior recombinants and selection of parents with wider variability for different traits. Therefore, there is a need to diversify the genetic base of improved rice cultivars. To this end, 30 rice genotypes comprising both drought tolerant and susceptible were screened with 50 rice microsatellite markers to estimate the genetic diversity of the genotypes. A total of 123 alleles were detected using 46 primer pairs with an average of 2.7 alleles per microsatellite locus, which was sufficient to classify the rice accessions investigated. In addition, they were also screened for drought tolerance using PEG-induced stress and data of root and shoot related traits viz., Root length, Root dry weight, Shoot length, Shoot dry weight, Root shoot weight ratio, Relative shoot length, Relative root length, Relative shoot dry weight, Relative root dry weight, and Relative root-shoot weight ratio were recorded. The genetic diversity of the rice genotypes was estimated using both molecular markers as well as drought related traits. The result from the present work is expected to give more insights in selection of parents for development of drought tolerant varieties.