In the present experiment, ten Egyptian wheat (Triticum aestivum L.) cultivars were used, i.e. Gemmiza 9, Gemmiza 10, Gemmiza 11, Sids 1, Sids 2, Misr 1, Sakha 93, Giza 168, Shakha 94 and Shakha 95. Morphological, chemical, biochemical, and molecular markers were used to detect the genetic differentiation among the cultivars under different salt levels on seedling performance. The results indicated that there are highly significant variations between the studied wheat cultivars. For RAPD-PCR analysis, a total of 75 bands were detected among the studied cultivars., 53 bands showed polymorphism and for SSR markers a total of 11 bands were detected among the studied genotypes and 8 bands showed polymorphism