The 1BL/1RS wheat-rye translocations had been used in wheat breeding programs worldwide. The objective of this study was to determine the effect of the 1BL/1RS translocation in SeriM82 /Babax recombinant population. 167 lines of this population were assayed under well-irrigated, terminal drought, heat and a combination of heat and drought stress conditions in two years. 5S rDNA and Iag95 markers were used to differentiate genotypes with or without the1BL/1RS translocation. Presence of 1BL/1RS translocation reduced grain yield (YLD), grain per spike (GSP) and grain per m2 (GM2). QTLs in 1 BL/1RS segments indicated increased thousand-grain weight (TGW), chlorophyll content, spikelet per spike (SPLS), spike compactness (SCOM) and awn length (AWL) but reduced YLD, GSP and GM2. The 1BL/1RS carrying lines’ response varied between assayed environments. Plants of drought trials were more affected by 1BL/1RS compared to others. Differences in the effects of 1BL/1RS and QTLs suggest that gene expression at translocation loci is restricted to specific environmental conditions. In general, the 1BL/1RS translocation could not be a suitable source of genetic diversity for enhancing grain yield under heat and drought stresses.