The global production of durum wheat (Triticum durumDesf.) is hindered by a constant rise in the frequency of severe heat stress. Three different germplasm panels were investigated under a range of heat stress to identify tolerant germplasm. The ‘discovery panel’ was field tested in the south of Morocco and along the Senegal River implementing a mild-to-strong North-South heat stress gradient. A subset of this same panel was also exposed to simulated terminal heat stress by applying plastic tunnels at the time of flowering. The ‘investigation panel’ and a ‘validation panel’ were field tested along the Senegal River under >32°C temperature throughout the season. Grain yield and its components were recorded at each site and a heat stress susceptibility index (HSI) was calculated. A total of 7,652 polymorphic single nucleotide polymorphisms (SNPs) defined the diversity of the first panel, while 5,642 SNPs defined the ‘investigation panel’. Genome-wide association study revealed that 36 quantitative trat loci were associated with the target traits in the ‘discovery’ panel, of which five were confirmed in the ‘subset’ tested with plastic tunnels and in the ‘investigation panel’. A haplotype study confirmed that Q.icd.Heat.003-1A, Q.icd.Heat.007-1B and Q.icd.Heat.016-3B are additive in nature and carrying the positive alleles at all three loci resulted in a 17% higher grain yield under heat stress. The underlying SNPs were converted into Kompetitive Allele Specific PCR (KASP) markers and tested on the ‘validation’ panel, confirming that each explained 4 to 9% of the phenotypic variation for grain yield under heat stress.