The key for rice plant survival under NaCl salt stress is maintaining a high K+/Na+ ratio in its cells. Selection for salt tolerance rice genotypes based on phenotypic performance alone will delay in progress in breeding. Use of molecular markers in tandem with physiological studies will help in better identification of salt tolerant rice accessions. Eight rice accessions along with the check Dongjin were screened using 1/2 Yoshida solution with 50 mmol/L NaCl at the seedling stage. The accessions IT001158, IT246674, IT260533 and IT291341 were classified as salt tolerant based on their K+/Na+ ratios. Seventeen SSR markers reported to be associated with K+/Na+ ratio were used to screen the accessions. Five SSR markers (RM8053, RM345, RM318, RM253 and RM7075) could differentiate accessions classified based on their K+/Na+ ratios. Banding pattern of the accessions was scored compared to the banding pattern of Dongjin. The study differentiated accessions based on their association of K+/Na+ ratio with molecular markers which are very reliable. These markers can play a significant role in screening large set of rice germplasms for salt tolerance and also help in identification of high-yielding varieties with better salt tolerance. The salt tolerant accessions can be taken forward into developing better varieties by conventional breeding and exploring genes for salt tolerance.