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Eleven genotypes, including the salt tolerant cultivar Pokkali as check, were used to evaluate salinity tolerance phenotypically and genotypically. Three selected SSR primers viz., RM7075, RM336 and RM253 were used to evaluate rice genotypes for salt tolerance. Two setups were maintained for this study viz., the seedling and reproductive stages. Phenotyping at the seedling stage was done in hydroponic system using salinized (EC 12 dS m(-1)) nutrient solution and at the reproductive stage using salinized tap water (EC 6 dS m(-1)). IRRI standard protocol was followed to evaluate salinity tolerance in rice. The genotypes having similar banding pattern with Pokkali were considered as tolerant. Phenotypically, three genotypes Pokkali, THDB and TNDB-100 and five genotypes RD-2586, TNDB-100, Dhol Kochuri, PNR-519 and Pokkali were identified as salt tolerant at the seedling and reproductive stages, respectively. These genotypes were also identified as salt tolerant genotypically (with markers). Through phenotypic and genotypic study, five genotypes viz., Pokkali, Dhol Kochuri, RD-2586, TNDB-100 and PNR-519 were identified as salt tolerant. Therefore, these microsatellite markers used in this study could be efficiently used for identification of salt tolerant rice varieties in marker-assisted breeding and quantitative trait loci analysis.