Exploitation of available genetic resources is of great importance for enhancing global food security under the adverse influence of climate change that badly affects the intensity of drought. A diverse group of hexaploid wheat genotypes (131) were evaluated for phenological and physiological traits in the field under well-watered and drought stress conditions imposed at anthesis stage along with check cultivars during two consecutive growing years, 2013-2014 and 2014-2015. Genotypes under both trial condition showed high genetic variation in their morphological and physiological indices in response to drought stress. Overall, 10 potential genotypes i.e. HU85, HU89, HU93, HU99, HU101, HU105, HU109, HU116, HU120 and HU123 outperformed among the evaluated genotypes. In terms of yield, these 10 lines performed 30% better than the best drought check cultivars (Weeble, Sitta and Dharwar-Dry) and therefore can be used as gene pool for varietal improvement for the rain fed areas of Pakistan. HMW-GS subunit composition and variation were analyzed at the Glu-1 locus through SDS-PAGE which detected eighteen alleles, 3 at the Glu-A1 locus, 11 at the Glu-B1 and 4 at the Glu-D1 locus with 34 different combinations. Twenty seven functional markers (KASP-SNPs) were also applied to identify important genes influencing end use quality including HMW-GS (3 NSPs), LMW-GS (15 SNPs), grain texture (3 SNPs) and drought tolerance candidate genes (6 SNPs), detecting a total of 61 alleles across the studied genotypes. SNPs for HMW-GS detected eight allelic loci among the genotypes and prominent alleles (5+10) were found in maximum (53%) genotypes followed by inferior (2+12) allele (40%). For LMW-GS, 25 SNPs loci were identified in the panel and the maximum allelic diversity was detected for Glu-A3ac (0.54%). Ample allelic diversity was observed at Ha loci encoding for hardness profile such as Pina-D1a (24%), PinaD1b (75%), PinbD1a (10%), PinbD1b (83%), Pinb-B2a (76%) and Pinb-B2b (16%), indicating the potential for selecting favorable alleles for enhanced grain texture. Thirteen candidate loci linked to drought related traits were detected which discriminated tolerant and susceptible genotypes through a set of six SNP markers. 1fehw3 detected Kauz-type (51.9%) tolerance followed by Westona-type tolerance (45%) across the panel. SST4D-1093 marker identified three allelic haplotypes, 4Da, 4Da:4Db and 4Db that favored stem WSC remobilization under low moisture status to minimize the deleterious effect of drought stress. The studied panel was profiled using 154 SSR markers for genetic diversity and GWAS. All of the 154 SSR markers were polymorphic in nature and detected a total of 254 informative loci. The average number of alleles per locus was 5.3, ranging from 2 to 13. The average effective number (Ne) of alleles per locus was 3.4, ranging from 1.1 to 7.8. Mean of expected heterozygosity (He) was 0.78, ranging from 0.10 to 1.9, information index (ID) ranged from 0.20 to 2.8, average, unbiased heterozygosity (UHe) value was 0.78 with a range of 0.10 to 1.9. The range for PIC was 0.18 to 0.87, with an average of 0.6 in the panel. A total of 347 significant MTAs for the studied traits were detected. GLM model approach detected 205 MTAs (59.2%) while MLM model approach found only 141 MTAs (40.6%). Some unique MTAs were also detected only either in GLM or in MLM model. Indel and SSR markers used in the current GWAS will contribute valuable information for AM panels and making new breeding populations based on marker assisted selection (MAS).