Bread wheat is the greatest vital crop for global population.An investigation to find out the genetic diversity among 102 wheat genotypes acquired from Plant Genetic Resources Institute of Pakistan. Agro-morphological data was noted for nineteen measurable traits at various growing phases in the winter 2016 in Mansehra District. The data was analyzed by applying Analysis of variance (ANOVA), Least significant difference test (LSD), Principal component analyses and cluster analysis. Results revealed significant level of diversity for all the morphological traits. Out of one hundred and two genotypes, a subset of eighteen has been established having quality characters. The genotypes were clustered into five groups clusters based on Euclidean dissimilarity index.PCA based on 19 morphological characters under 2016 year displayed that first 5th PCs accounted for 55.83% of total variance, PC I, PC II, and PC III showed maximum genetic variability 18.15%, 13.33%, 10.78% respectively of total morphological diversity. Wheat seedling were also screened for drought tolerance through Relative water contents (RWC), Water loss rate (WLR), Water use efficiency (WUE) and selected root traits. The genotypes seemed to respond differently during drought and normal environment for physiological and seedling traits. Under drought stress condition PS-05, PS-08, Atta Habib, 10770 and 10779 were considered as drought tolerant due to their high relative water contents, lower water loss rate and higher water use efficiency. Under drought condition shoot length, root length, root fresh weight, and root dry weight, shoot fresh weight, and root dry weight decreased by 30.95, 31.26, xiii 47.20, 55.03, 37.25, 34.18%, respectively. Significant and positive correlation was found among most of the seedling traits under normal and stress conditions. The genotypes PS-05, PS-08, Atta Habib, 10770, 10779, 10761, and 10785 were screened as drought tolerant while Faisalabad-08, Sehar-06, Lasani-08, 011870, 011872, 011871, and 011869 as drought susceptible genotypes. Out of 58 SSR markers used for estimation of genetic diversity 47 showed polymorphism. The dendrogram was created based on coefficient of similarity using UPGMA analysis. Per locus an average alleles were 7.027 detected. Per marker with an average of 0.84 of PIC values were observed. It was concluded from the results that microsatellite markers were effective in detect polymorphic marker with high genetic similarity in wheat. Two drought responsive candidate genes (Dehydration-Responsive Element Binding (dreb), and Fructan exohydrolase (Feh), were amplified using KASP. Out of the 102 genotypes, 61 were found to carry the allele A (dreb – resistant allele) which refers to the Dreb gene, while 33 genotypes were found to carry the allele C (feh – resistant allele) which is highly expressed under drought stress.Our results demonstrated the relative importance of several morphological, physiological, root traits, SSR, and KASP markers using dreb, feh gene for drought resistant evaluation in genotypes of wheat. This study offers claims to cultivate drought tolerant genotypes for food security in drought prone environment.