Ten ISSR and SCoT primers were used to estimate the genetic variability between some Egyptian wheat genotypes. A total of (141) bands across both types of markers, of which 72 ISSR bands (87.5%) and 69 SCoT bands (81.1%) were polymorphic. ISSR showed higher levels of polymorphism (P%), indicating its efficacy in separating closely related germplasm. The polymorphism information content (PIC) and resolving power (Rp) indicated no preference for any type of markers. Effective multiplex ratio (EMR), marker index (MI) indicated that ISSR revealed higher values. SCoT1 primer showed the highest P%, PIC, MI and EMR values while SCoT12 showed the highest Rp values. While, HB-11 primer showed the highest MI and EMR values, 98-A primer showed the highest P% and PIC. Across the two types of markers, a total of 54 genotype-specific markers were amplified. Most markers were showed by Shandaweel 1 genotype. Some of these markers are related to drought tolerance, and also, can be used in detecting possible relatedness among genotypes. We had profiled the expression of seven TaWRKY genes under PEG6000 stress. High variation in gene expression was observed between Shandaweel 1and Misr 3. All TaWRKY genes were expressed under different concentrations of PEG for Shandaweel 1, while Misr 3 was up regulated for all studied genes except for TaWRKY50. The relative TaWRKY genes expression showed highest and lowest levels in Shandaweel 1 and Misr 3 respectively. Moreover, TaWRKY44 upregulated under all studied concentrations of PEG except for Shandaweel 1 at 15 % PEG, while TaWRKY50 was downregulated for both genotypes under all studied concentrations except for Shandaweel 1 at 15 %PEG. Generally, we demonstrated high genetic variability through DNA marker, and variable gene expression studies between the studied genotypes.