Abstract: Background and Objective: Wheat and barley considered very important cereals for 100 millions of Egyptian population. Therefore, yield improving of some Egyptian varieties via genetic markers cereal crops under abiotic stresses drought and salinity is a crucial objective of this research. Materials and Methods: Five varieties of quadruple wheat were evaluated under salt stress and 14 varieties of barley were evaluated under drought stress to determine the genetic mechanisms related with molecular markers responsible for salinity tolerance in wheat and water deficit in barley. The techniques used were RAPD, ISSR and SSR-PCR, the obtained data of items studied were analyzed by molecular methods. Results: The results obtained from SSR revealed the presence of five molecular markers related to water stress tolerance in barley, three of which were positive for endurance and durability compared with control. While, RAPD-PCR revealed 3 markers which have 2 positive and one negative with primers OPE-26, E-10 and A-12, respectively. Furthermore, molecular studies of quadruple wheat for salt tolerance revealed the presence of 15 molecular markers from RAPD-PCR and ISSR techniques, six of which were positive with Beni-Sweif4, while Beni-Sweif1, 3 and Beni-Sweif5 had two positive markers for each of them. Conclusion: It could be concluded that RAPD, ISSR and SSR markers played vital and successful role to identify between all the genotypes used concerning salt stress in wheat and drought stress in barley, which could be helpful in the enhancement of cereals production in Egypt. This technology can be used as an indicator of molecular breeding in barley and wheat. This stage is the strategic bit for increasing the ability of abiotic stress tolerance of the studied lines and using it in local breeding programs.