salinity is considered as one of important physical factors influencing rice (Oryza sativa L.) production. Knowledge of salinity effects on rice seedling growth and yield components would improve management practices in fields and increase our understanding of salt tolerance mechanisms in rice. This study was designed to assess the role of Saltol QTL in regards to effects of salinity on plant growth and yield components of different genotypes of rice at different growth stages. A greenhouse study was conducted to evaluate the response of 30 rice genotypes to three levels of salt stresses (0, 60, 100 mM NaCl) at reproductive stage. The seedling stage response of these genotypes to salinity with electrical conductivity at 12 dSm-1 also investigated. Pollen viability, number of unfilled and filled grain and grain yield per plant were evaluated. The rice genotypes differed significantly for salt tolerance at seedling stage. The genotypes were also significantly varied for the traits measured at the reproductive stage. The interactions of genotypes × salinity treatments were significant for pollen viability, number of unfilled grain and grain yield. Grain yield reduction due to salinity was more sever for control to 60mM than for 60mM to 100mM. Pollen viability was found to be a robust criterion to screen the genotypes for salt tolerance at the reproductive stage. Pokkali cultivar possessing a major quantitative trait locus (QTL) for salt tolerance at seedling stage (Saltol) mapped on chromosome 1 was used as reference for haplotyping. Thirty rice genotypes divided into 16 different haplotypes based on Saltol QTL. RM8094 and RM10745 microsatelite markers found to be the most effective markers for discriminating the salinity tolerant genotypes.