Determining and improving drought-tolerant cultivars is a major goal of plant breeding to face climate change. The productivity of faba bean in Egypt is affected by abiotic stresses, especially drought stress. This study evaluated eight Egyptian faba bean cultivars for drought tolerance under three soil water regimes consisting of well-watered (100% field capacity), moderate drought stress (50% field capacity), and severe drought stress (25% field capacity) regimes in pots under greenhouse conditions using biochemical, physiochemical, and molecular parameters. The cultivars Nubariya 1, Nubariya 3, and Giza 716 showed the highest proline content values under 50% field capacity conditions, with 4.94, 4.39, and 4.26 mmol/g fresh weights, respectively. On the other hand, the cultivars Sakha 1, Sakha 4, Nubariya 1, and Nubariya 3 exhibited the highest proline contents (7.8, 7.53, 6.17, and 6.25, respectively) under 25% field capacity treatment. The molecular profiling was conducted using SCoT and SRAP approaches. Fresh leaves were utilized to extract the DNA, and ten primers for SRAP and six for SCoT were used in the PCR procedures. SCoT and SRAP-PCR generated 72 loci, of which, 55 were polymorphic, and 17 were monomorphic. SCoT and SRAP each had 48 and 24 total loci, respectively. The average polymorphism (%) values achieved via SCoT and SRAP were 70.93% and 80%, respectively. Based on the molecular profiles, the cluster analysis identified three clusters. The first cluster comprised Giza 716 cultivars; the second cluster included Sakha 1, Sakha 3, Sakha 4, and Akba 3300 cultivars; the third cluster comprised two cultivars Nubariya 1 and Nubariya3. According to the study’s findings, Sakha 1, Sakha 4, Nubariya 1, and Nubariya 3 are remarkable parents for developing drought-tolerant faba bean genotypes. Additionally, this study concluded that SRAP and SCoT markers recreated trustworthy banding profiles to evaluate the genetic polymorphism among faba bean cultivars, which are regarded as the cornerstone for genetic improvements in crops.