The wheat is a staple food of Pakistan and drought is a major problem not only of Pakistan but whole of the world. The study was conducted in the department of Plant Breeding and Genetics, University of Agriculture Faisalabad. In total 226 genotypes were grown in polythene bags and drought stress was imposed using PEG-6000 (20%) and data were collected for shoot length, root length, root shoot ratio, fresh weight and dry weight. The genotypes which showed good performance for all the parameters were selected (100 genotypes) and evaluated during the next two years 2013-14 and 2014-15 under both the normal and meiotic stage (pre-anthesis) drought stress conditions. The data were collected for 14 traits such as days to heading, days to maturity, plant height, peduncle length, spike length, length, width and area of the flag leaves, spikelets per spike, grains no. /spike, grain weight /spike, tillers per plant, thousand grains weight and yield /plant. Principal component analysis was used to derive the information regarding variation in the germplasm. ANNOVA exhibited that all the differences were significant for all the parameters under both the normal as well as the drought conditions during first and also during 2nd years. The first and second PC being the most diverse components showed 28.4% and 42.2% of variation during 2013-14 under normal conditions and 13.6% and 33.7 % under drought conditions in the same year. Biplot based on the 2013-14 data collected under normal conditions represented that the heading days, length of the peduncle, length of spikes, area of the flag leaves, and the weight of 1000 grains and no. of spikelets / spike contributed greatly in diversity. Yield per plant showed significantly positive results of correlation with grains / spike and tillers / plant under stress environments. Similarly under irrigated conditions leaf length was affected negatively for the data collected during 2013-14. During 2014-15 the yield of the plants had shown the significant correlation but in negative direction with the trait like length of the spike, leaf width and 1000 grain weight stress conditions while under normal conditions yield per plant showed the correlation that was significant and in positive direction with that of time taken to the maturity and the duration to the heading of the crop while significant results of yield for correlation but in negative direction with peduncle length, spikelets per spike and tillers per plant. The study showed the behavior of different traits under irrigated and stressed conditions and can be helpful to identify the traits which are affected under stress. The structure analysis divided the 100 genotypes into three sub populations containing 50 in first and 25 genotypes in 2nd and 3rd population respectively. The molecular work showed that eight characters were identified which were linked with nine SSR markers at probability level of 1% and the phenotypic value was in range of 14 to 32% under water stress conditions. But under the irrigated conditions the same genotypes showed that six parameters were linked with six SSR markers with the same probability level and phenotypic variability was ranged from 14% to 22%. The five SSR primers were identified such as WMC382, CFA2086, CFA2121, CFA2263 and WMC2610 which were linked with spikelets per spike which can be concluded as trait specific MTA.