Salinity is one of the most important factors limiting agricultural production. Cotton, as an oil-fiber plant, is one of the most important industrial plants and is sensitive to salinity, especially at germination and seedling stages. Therefore, in this study, 14 allotetraploid varieties of commercial and local cotton were selected. The study was carried out as factorial with a completely randomized design and three three replications, using the sandwich method. Germination tests were performed at three salinity levels of 0, 8 and 16 ds.m^-1. Afterwards, root and shoot length, fresh and dry weight of root and shoot, germination percentage, allometric coefficient, seedling water percentage and seed vigor index were measured and stress tolerance indices were calculated based on yield (seedling dry weight) in stress and non-stress conditions. Given these indices, all cultivars were aalyzed at two levels of 8 and 16ds.m^-1, using principal component analysis and biplot diagrams were drawn. Finally, the dendrogram classification of genotypes was plotted based on STI indices (stress tolerance index), SSI (stress susceptibility index), and the performance (dry weight plantlet) in stress and non-stress conditions. The result of variance analysis for genotype, salinity and salinity×genotype demonstrated that dry weight root, dry weight shoot, fresh weight root, stem length, vigor index seedling, allometric coefficient, dry weight seedling, and length seedling were significant in p-value 0.01, and fresh weight shoot, length root were significant in p-value 0.05. Clustering and the biplot of the genotypes based on STI and SSI indices at salinity levels of 8 and 16 ds.m^-1 indicated that the Sepid and Giza genotypes were tolerant and that the Kashmar genotype was sensitive to salt levels at germination stage.