Egypt is a good area to study related wheat species in order to improve bread wheat features because it is one of the most important genetic and distribution centers for wheat species. Agronomic parameters, ISSR (inter simple sequence repeats), and SCGE were used (Single Cell Gel Electrophoresis), to study abiotic challenges such as drought. Climate change has increased the impact of drought stress on wheat production, which affects plant growth and development, grain formation, grain quality, and eventually yields. Drought stress has been adapted to by plants in a variety of ways, including genetic adaptations. Four potential wheat lines were tested for genetic diversity and molecular marker identification. There was significant variation in most agronomic traits. Four wheat cultivars (Sakha-8, Gemmiza-7, Giza168, and Sids-1) were subjected to watering levels of 20, 60, and 100% in this study. The Comet assay results revealed that Gemmiza-7 produced low-tailed DNA (8 %), indicating its drought resistance when compared to other varieties. The ten ISSR primers used achieved a rate of polymorphism ranging from 62.5% to 100%, with an average of 83.3% for all primers. Our findings with ISSR molecular markers tested pointed to some distinguishing and unique bands that could be used as cultivar selection tools.