The present study was carried out on spring wheat germplasm to mine the nature and magnitude of morphological diversity and LD based association between markers and seed traits influencing the end use quality of wheat. The diversity patterns among 245 genotypes on the basis of phenotypic data revealed the extent of diversity which can be exploited for future breeding programs. Out of fourteen quantitative traits phenotyped, protein content, gluten content, starch and test weight contributed towards significant principal components (PCs) with highly significant correlation with chapatti and bread quality. Whereas, seed size and thousand grain weight were strongly associated with grain yield per plant. On the basis of principal component analysis, a set of 143 diverse genotypes was selected for SDS-PAGE analysis for HMW and LMW glutenin subunits. The frequencies of various HMW-GS were different for Pakistani landraces and modern Pakistani and CIMMYT germplasm. Landraces had a good chapatti quality and an overall poor bread quality while, the modern germplasm from both Pakistan and CIMMYT displayed good quality for both chapatti and bread. The correlation pattern between seed traits was similar in CIMMYT and Pakistani germplasm. Landraces and miscellaneous germplasm had different pattern of trait association from those of CIMMYT and Pakistani germplasm. On the basis of PCA and gluten protein profiling, 92 diverse genotypes were selected for subsequent association mapping. Population structure was detected with 30 unlinked SSRs that divided the population of 92 genotypes in three sub- populations. Extensive LD extent was found with 42 SSRs specific for 1B chromosome. Six SSR markers were found associated with six seed traits. In addition to finding novel markers, the results of association mapping from the study also confirmed previous results. The markers which were found significantly linked to the six quality traits may be used efficiently for the improvement of these traits through MAS.