Wheat stem rust, caused by Puccinia graminis f. sp. tritici, and yellow rust, caused by Puccinia striiformis Westend. f. sp. tritici Erikss. (Pst), are the most important wheat diseases. The study used molecular characterization and identification of candidate lines and cultivars for predicting stem rust and yellow rust resistance genes (Sr2, Sr28, Sr35, Sr40; Yr10, Yr15 and Yr18), respectively. The result of this study showed that the analysis of four Egyptian cultivars and three Libyan local cultivars and three advanced breeding lines from CIMMYT and ICARDA for a marker linked to individual gene, Sr2 was present in all test genotypes, Sr28 was present in six genotypes, Sr35 was present in four genotypes,Sr40 was present in two genotypes. Likewise, Yr10 was present in two genotypes, Yr15 in six genotypes and Yr18 wasn't found in any of the tested genotypes. These markers should be useful in marker-assisted pyramiding of stem rust and yellow rust resistance genes to develop new cultivars with multiple gene resistance against stem rust, yellow rust races in Egyptian wheat.