Polyethylene glycol and cell membrane stability (CMS) assay were used to evaluate drought and heat tolerance, respectively, among 14 wheat lines based on seedling traits and molecular analysis. Significant variation was evidenced for all the investigated seedling traits. Different levels of heritability and genetic advance were found among the tested traits, indicating whether the trait is controlled by additive or non-additive gene action. Drought caused a significant reduction in root and shoot lengths. However, root/shoot ratio under drought stress was increased. Root length showed a highly significant negative correlation with drought susceptibility index (DSI) under drought conditions. Cluster analysis based on seedling traits separated lines mainly by DSI and CMS. Some lines showed drought and heat tolerance by exhibiting a low DSI with high CMS. Sequence-related amplified polymorphism (SRAP) generated a total of 135 bands, with a level of polymorphism ranging from 30 to 86% among the tested lines. SRAP showed its efficiency in discriminating wheat genotypes by gathering all high-DSIlines in one sub-cluster and generating 10 and 3 unique and specific bands for high-DSI-lines and low-DSI-lines, respectively. These bands could be used for further work as SRAP markers associated with drought tolerance in wheat.