This is an Open-Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. ABSTRACT 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 (bi=1 and S 2 di = 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 (bi = 1.