<p>Drought stress significantly reduces wheat yields, making it a critical factor for agricultural productivity. To enhance crop improvement programs in the context of changing climate conditions, it is vital to simultaneously evaluate genetic and environmental factors. While conventional breeding methods are widely used, the limitations of these approaches have led breeders to adopt Molecular Marker-Assisted Selection to identify drought-tolerant varieties. In this study, we evaluated 31 wheat varieties over three cropping seasons under both rainfed and supplemented irrigation conditions, employing a randomized complete block design with three replications. We assessed drought tolerance indices and performed molecular analyses using 11 SSR primers to identify drought-tolerant wheat varieties. The combined analysis of variance indicated significant differences in grain yield among the varieties across the six environments studied. Cluster analysis based on drought tolerance indices classified the varieties into three distinct groups over the three cropping seasons. Notably, all SSR primers demonstrated 100% polymorphism. Among the marker indices such as polymorphism percentage, PIC, EMR, MI, and RP, the most informative primer was xbarc230. Furthermore, cluster analysis and Principal Coordinate Analysis (PCoA) using the Dice similarity coefficient organized the varieties into six and four groups, respectively. Based on the assessment of drought tolerance indicators and molecular data from SSR analysis, Alvand and Marvdasht were identified as semi-tolerant varieties, while Shahpasand and Sardari were classified as drought-sensitive. Parsi was recognized as a drought-tolerant variety with high yield potential. In conclusion, this research provides valuable insights for breeders aiming to develop drought-tolerant wheat varieties.</p>