Soil salinity is one of the major production constraints. Development and planting of salt-tolerant varieties can reduce yield losses due to salinity. We screened 185 rice genotypes at germination stage in petri dishes under control, 50, 100 and 150 mm salt stress, and at seedling stage in Yoshida's hydroponic nutrient solution under control, 50 and 100 mm salt stress. At germination stage, 15 genotypes including Nona Bokra, Sonahri Kangni, 7421, 7423 and 7467, whereas at seedling stage, 28 genotypes including Nona Bokra, Jajai-77, KSK-133, KSK-282, Fakhr-e-Malakand, Pakhal, IR-6, Khushboo-95, Shahkar and Shua-92 were found salt tolerant. Basmati-370, Mushkan, Homo-46 and accessions 7436, 7437 and 7720 were sensitive to salinity at both germination and seedling stage. We further screened a subset of 33 salt-tolerant and salt-sensitive genotypes with SSR markers. Four SSR markers (RM19, RM171, RM172 and RM189) showed significant association with two or more of the studied traits under 50, 100 and 150 mm salt stress. These markers may be further tested for their potential in marker-assisted selection. The salt-tolerant genotypes identified in this study may prove useful in the development of salt-tolerant rice varieties in adapted genetic background.