Genome-wide association mapping shows promise for identifying quantitative trait loci (QTL) for many traits including drought and heat stress tolerance. During first cropping season, seven International Maize and Wheat Improvement center (CIMMYT) bread wheat nurseries were screened under rain fed conditions and based on high 1000 kernel weight and parentage diversity 108 high yielding lines were selected further evaluation. Wheat performance was checked at two growth stages i.e. seedling and post anthesis, at seedling stage stress was imposed by using two different potentials (-3bar and -6 bar) of polyethylene glycol (PEG 6000) and heat stress 36Cº for 3hrs daily. At post anthesis, three stress treatments including individual drought, individual heat and combination of drought and heat stress were imposed in glass house and open field conditions. The data was recorded for seedling, yield traits, physio-biochemical traits and stress related traits for two consecutive cropping seasons (2014-2015 and 2015-2016) at the National Agriculture Research Center (NARC) Islamabad. The germplasm was genotyped with high-density Illumina 15k single nucleotide polymorphism (SNP) chip to identify genomic regions associated with traits under drought, heat and combined stress. Total 9464 highly polymorphic markers were used for calculation linkage disequilibrium, population structure and marker trait associations. Structure analysis divided germplasm into 5 major clusters and highest rate of linkage disequilibrium was recorded for D genome due to its recent origin. Mixed linear model (MLM) with kinship matrix as covariant is used to calculated maker trait associations best linear unbiased estimates (BLUEs) values. For seedling traits significance threshold was log10(P)>3.0 while for pot and field experiment significant threshold was set by xxii using standard (1/n, n= no of markers) method and significance of an association was further checked by using FDR < 0.05 threshold. For seedling trait 1191 association significant beyond threshold were recorded most of these were concentrated on chromosome 7D. For traits studied in post and field experiment 300 and 105 significant associations (beyond p value threshold) were recorded while 128 associations in the pot experiment crossed FDR significance threshold and 35 MTAs were significant at FDR under field condition. Fifty-four and nineteen pleiotropic region associated with multiple traits were recorded under pot and field experiment respectively. Significant MTAs detected in the present study were similar as reported by the previous studies while some differ with respect to their chromosomal position. The MTAs detected in combination of drought and heat stress can be helpful in marker assisted selection to improve drought and heat tolerance of wheat.