Soil salinity is the second most important abiotic stress having a drastic effect on agricultural yield. None of the rice varieties possess all the possible positive mechanisms conferring salinity tolerance. Eleven high yielding salt tolerant rice varieties (VTL-1, VTL-2, VTL-3, VTL-4, VTL-5R, VTL-5W, VTL-6, VTL-7, VTL-8, Ezhome-1, Ezhome-2) released from Kerala Agricultural University were screened for seedling stage salinity tolerance based on modified Standard Evaluation Score (SES) developed by International Rice Research Institute, Manila, Philippines. Pokkali (Ac.No. VTL 505), a saline tolerant landrace and Jyothi, a popular rice variety of Kerala were included as tolerant check and susceptible check varieties respectively. Based on the visual scoring of rice varieties under saline conditions, the varieties VTL-1, VTL-2, VTL-5R, VTL-5W and VTL-6 were classified as saline tolerant whereas VTL-3, VTL-4, VTL-7, VTL-8, Ezhome-1 and Ezhome-2 as moderately saline tolerant varieties. Phenotypic traits of these varieties were also studied under salt stress and non- stressed conditions and it was found that tolerant varieties were less affected compared to the moderately tolerant varieties. Tolerant varieties showed a great increase in root length with a minimum decrease in shoot length and dry weight under salinity stress. SSR marker analysis with 27 SSR markers including the Saltol specific markers on chromosome 1 indicated a moderate degree of polymorphism among the rice varieties. Cluster analysis of the eleven rice genotypes based on SSR data revealed the closely and distantly related salt tolerant rice varieties.