Bread wheat (Triticum aestivum; of 2n=6x=42) having hexaploid genome (AABBDD) of 17 Gb is the major staple food of Pakistan. The wheat production in Pakistan shows a long standing instability due to drought stress in wheat growing season. The introduction of drought tolerant commercial varieties is therefore the cry of the day, which needs marker assisted selection evolving promising lines. This dissertation communicates the results of a research endeavor based upon evaluation of 100 wheat accessions for drought stress under lab and field conditions. The data was obtained on morphological, physiological and marker associated assays for genome wide association mapping of the major alleles against drought. Reults of the morphological analysis showed that genotype Bahawalpur-79 ranked first on the basis of days to maturity, Barani-70 showed highest number of tillers, Marwat-01 has highest spike length, Margalla-99 has greatest spikelets per spike, Zarghoon-79 has highest 1000 grain weight and C-273 have highest harvest index and Uqab-2000 showed optimum plant height. These genotypes could be used for further breeding programs to improve wheat production under drought stress conditions of Pakistan. Analysis of Variance of the physiological data provided highly significant differences among the genotypes both in normal and drought stress. Margalla-99 recorded the highest relative water content in normal while NIAB-83 recorded the highest relative water content in drought stress conditions. Faisalabad-83 and Iqbal-2000 was ranked first on the basis of water loss rate in normal and water loss rate in stress conditions while NIAB-83 was ranked first in water use efficiency test. These genotypes may be recommended for commercial cultivation in irrigated and rainfed areas of Pakistan. The correlation analysis revealed that root dry weight, maximum root length, total root length, root shoot ratio, root diameter and number of seminal roots were positively correlated with water loss rate stress and relative water content stress and considered to be best root traits for drought tolerance. Pirsabak-85, AS-2002, Abdaghar-97, Marwat-01 and Soghat-90 were ranked first on the basis of root traits and considered to be best for drought stress areas of Pakistan. All the genotypes were screened with 102 SSR markers in which most of the markers were showed high level of polymorphism. Sum of 271 polymorphic alleles generated. The alleles per locus ranged from 1-3 with an average of 2.63 per locus. Polymorphic Information Content (PIC) values of the markers were calculated in the range of 0.03–0.59. The association analysis through linkage disequilibrium of 100 accessions clustered into thirteen distinct groups. Our analyses identified significant association between Xgdm5 and total root length, Xwmc235 and root fresh weight, Ppd-D1 and root dry weight, Xwmc149 and maximum root length, Xwmc175 and number of nodal roots, Xgwm302 and root angle, Xwmc175 and root density and Xwmc233 and root diameter. All the marker/trait associations were located on seven chromosomes (2D, 5B, 2A, 2B, 7B, 6D and 5D. The marker/trait association for maximum root length was not reported previously. The genetic information obtained might be used in marker-assisted selection to improve drought tolerance of wheat.