The genetic variability and yield stability are complex traits with large environmental components that are utilized for breeding of improved plant performance under drought conditions. In order to better understand the relationship among genotype, trait components, and environment, marker-trait associations in 20 wheat varieties using phenotypic and ISSR (Inter-Simple Sequence Repeat) markers under drought conditions were examined. The combined analysis of variance results showed that the tested traits were significantly influenced by years, irrigation treatments, and the varieties. The drought stress conditions resulted in a substantial reduction in grain yield by 33.70%. The varieties viz., Shakha-93, Sahel-1, Giza-160, Giza-168, Sids-1, Sids-4 and Nilen were relatively drought resistant (DSI, Drought Susceptibility Index values< 1) and gave high grain yield when compared with the average of all varieties under drought stress. The stability analysis revealed that the cultivar named ‘Sids-1’ showed high and stable yield (b_i=1 and S²d_i = 0), so it could be selected to be grown under drought stress conditions. On the other hand, Shakha-92 and Bacanora-88 showed below-average stability (b_i = 1.35 & 1.42), indicating that these genotypes perform well under normal conditions. The percent of polymorphism (%P) among varieties ranged from 25 to 80% with an average of 52.08%. Polymorphism information content (PIC) values varied from 0.08 to 0.28. Plant height and 1000-kernel weight showed significant regressions (23.83 and 27.54) under normal irrigation conditions, respectively. Moreover, under drought stress conditions, plant height, 1000-kernel weight and no. of spikes/m² showed significant regressions of 40.38, 20.95 and 24.95, respectively.

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