T HIS STUDY was conducted to point out some highlights on the difference between two contrasting tolerant wheat varieties regarding to genetic expression and molecular characterization under salt and drought stress. Two different tolerant wheat genotypes namely, Gemmiza9 (sensitive) and Sakha93 (tolerant) were used to investigate the molecular and genetic differences under salt and drought stress. Stress treatments were used NaCl and poly ethylene glycol (PEG) of different levels. Sodium dodecyl sulphate polyacrylamide gel electrophoresis(SDS PAGE) analysis was revealed three disappeared bands with 15, 25, 90 kilodalton (KD) in salt treated plants of Gemmiza9 and appeared these bands as constant in controlled and salt treated plants of Sakha93. Contradict vision for protein profile was under drought stress that constant bands were disappeared and new synthetic bands were exhibited in both Gemmiza9 and Sakha93. Moreover, Random amplification of polymorphic DNA (RAPD) markers were produced several number of unique bands in Sakha93. Primer 2 generated unique bands in Gemmiza9. Simple sequence repeats (SSR) markers were 100% polymorphism. WMC_179 marker out of six markers was present unique alleles only in Sakha93. This marker might be practical and advantageous to the genotype that recognized to tolerance QTL markers alleles to utilize in marker assisted selection in further study. Comparison between RAPD and SSR markers was revealed that QND was less (0.06) in RAPD than in SSR (0.56). EMI was higher (0.31) in RAPD than in SSR (0.23). Nonetheless, the findings might be valuable and helpful to identify the genetic and molecular characterizations of different tolerant genotypes.