To develop crop plants with enhanced tolerance of drought stress, a basic understanding of physiological, biochemical, and genetic networks is essential. Four bread wheat genotypes and one wheat line were evaluated for molecular indicators of drought tolerance using RAPD-PCR and protein profiling. The RAPD markers were used to determine the genetic differences between the five wheat genotypes and to determine the molecular markers associated with tolerance to drought. The present study found that RAPD analysis is a valuable diagnostic tool when different sets of RAPD primers were used to study the polymorphism at the molecular level. A total of 72 alleles were amplified with six random primers out of which 61% were monomorphic and 38% were polymorphic. Primer B8 amplified a 600 bp band in Sham-6 which is assumed to be a drought-tolerant genotype, while primer A-8 amplified a 550 bp band in genotypes Giza-168 and Sham-6. Genetically, the most similar genotypes were Sham-6 and Line-7 (93%) followed by Gemaza-9 and Giza-168 (92%) while the most dissimilar genotype was Sakha-93 (86%). Protein profiling revealed differences between the genotypes with a protein band presents at 130 KDa in the Sham-6, Gemaza-9, and Sakha-93 genotypes and absent in Line-7 and Giza-168. Proline content was highest in the drought-tolerant genotypes, Sham-6 and Sakha-93. Sucrose content in shoots was increased in tolerant plants (Sakha-93 and Sham-6), while there was a reduction in sucrose in the shoot tissues of the seedling stage of Gemaza-9, Line-7, and Giza-168. Overall, the accumulation of reducing sugars was lowest in all plants compared with sucrose content.