Identification of quantitative trait loci (QTL) and markers associated with heat and drought tolerance is warranted for marker-assisted selection in wheat (Triticum aestivum L.) breeding programs in areas prone to these abiotic stresses. Our study used a family-based mapping approach in which 19 families consisting of 384 individuals were developed by threeway crosses involving the heat tolerant, tetraploid cultivated emmer (Triticum turgidum L. var dicoccum) genotype IG45069 and ten heat susceptible tetraploid genotypes, IG44999, IG44961, IG45413, IG83047, IG45441, IG127682, IG45448, IG110572, IG88723 and IG54073, in order to detect QTL and markers associatedwith heat tolerance.The 384 individualswere phenotyped for physiological traits associated with heat tolerance and genotyped by SSR markers. The QTL associated with heat stress tolerance, as measured by chlorophyll content, flag leaf temperature depression (FLTD) and individual kernel weight (IKW) were mapped on chromosomes 1B (QChlc.tamu-1B), 2B (QFlt.tamu-2B), and 5A (QIkw.tamu-5A), respectively, using linkage analysis. Alleles from IG45069 possessed the highest associations with the phenotypic data for the studied traits. This study demonstrates that a family-based mapping approach can be utilized in rapid detection of QTL associated with heat tolerance in wheat based on linkage and association analyses.