Water deficit is being the most devastating abiotic stress factor in newly reclaimed soils in Egypt. Identification of useful alleles in both cultivated varieties and wild relatives of these traits might be helpful in developing drought tolerant genotypes. 301 doubled haploid (DH) lines, their parents (Scarlett and ISR 42-8) and four check cultivars were investigated under two water regimes in the 2013/2014 season in newly reclaimed area at Wadi Al-Asyouti farm of the Faculty of Agriculture, Assiut University, Assiut, Egypt. The QTL analysis revealed 35 putative QTLs as maker main effect and marker × treatment interaction for six studied traits. 17 QTLs were identified with favorable effects of the exotic alleles. Numerous interesting QTLs were detected in this study that displaying beneficial effects of the exotic alleles (Hsp). For instance, the alleles of the QTL QHD.S42-2H exhibited a favorable performance of reducing days to 50% heading by -3.03%. A favorable QTL QPH.S42-7Ha effect was responsible for almost 6.29% decrease in plant height due to Hsp alleles. Interestingly, the QTL QGYP.S42-1Ha revealed that marker × treatment interaction effect and the relative performance of the exotic genotype led to increase grain yield per plant with 14.31%. Altogether 21 pairs of epistatic QTLs as additive × additive effects were detected in current study. The majority of the digenic epistatic interaction pairs had favorable effects on the phenotypic values of the studied traits. For example, the most favorable pair of epistatic QTL for reducing heading date was bPb-9111* bPb-8701 and located on chromosomes 3H (141.94 cM) and 4H (93.64 cM) and accounted for 19.36% of genetic variation. The DH lines carrying the Hsp/Hsp combination at two loci had heavier grain weight by maximum 0.87 g more than lines with the allelic combination Hv/Hv. This study has highlighted the role of the exotic alleles for the detection of favorable alleles lead that for drought tolerance in barley.