<p>Rice is one of the most widely cultivated crops globally, serving as a primary food source for more than half of the world’s population. However, Salt stress can significantly reduce rice yields, affecting grain quality and quantity. Developing salt-tolerant rice varieties is crucial to mitigate the adverse effects of soil salinization and ensure food security. The phenotypic screening and the application of molecular markers also offer great potential for genetic improvement in rice for salt tolerance. Hence, the present investigation was carried out to evaluate thirty selected rice genotypes for assessment of their salt tolerance at early seedling stage through in vitro seed germination and seedling growth at different salt levels (0, 4, 8, 12 and 16 dS m^− 1) created by a salt mixture of NaCl, CaCl₂, Na₂SO₄ in 7:2:1 ratio. The phenotypic evaluation revealed that out of 30 genotypes, 18 were highly tolerant, 7 genotypes were moderately tolerant, and 5 genotypes were highly susceptible to salt stress. The salinity tolerance index (STI), the value calculated based on seedlings growth parameters namely shoot and root fresh and dry weight revealed that the genotype Pokkali with a mean STI value of 85.11 was the most tolerant genotype, whereas the Kalinga-3 with a mean STI of 40.49 was the most susceptible genotype under different levels of salt stress. A dendrogram based on dissimilarity coefficient of salt tolerance indices in pair-wise combinations for 30 genotypes revealed 3 major clusters designated as A, B and C. Clusters A and B included the genotypes categorised as highly tolerant and moderately tolerant as per STI values, and Cluster C had genotypes having lower STI value which was considered as highly susceptible genotypes. From a total of 30 genotypes, 18 contrasting sets of genotypes comprising 10 highly tolerant, 5 highly susceptible, and 3 moderately tolerant genotypes were subjected to genotyping using reported salt-responsive EST-contigs-based markers. However, the agarose gel-based survey did not reveal an informative amplification pattern between the contrasting set of rice genotypes. Six, out of eight markers were completely monomorphic in all the 18 selected genotypes and 2 markers showed dominant type polymorphism where the amplification was absent in two genotypes namely CSR-36 (highly tolerant) and MTU-7029 (moderately tolerant). As the early-stage screening in rice for salt tolerance is an efficient and proven approach for the identification of tolerant genotypes, the present study was successful in the identification of contrasting sets of rice genotypes comprising highly tolerant and highly susceptible bulks which can be utilized in breeding programs of rice for salt tolerance. Our results demonstrated significant genetic diversity among the rice varieties for salt tolerance, which can be exploited for breeding programs.</p>