India is the second largest producer of wheat in the world after China. The quality of Indian wheat needs improvement not only for domestic consumption but also for meeting international standards for export purpose. Both RAPD and ISSR markers are found to be efficient to assess genetic diversity within and between species of wheat. Glutenin protein SDS-PAGE found efficient to detect polymorphism among wheat cultivars for dough quality. Cultivars GW-273 and GW-322 showed highest Glu-1 score of 10 out of 10, indicating superior dough quality for bread making. Allele Dx5+Dy10 were found to be responsible for good dough quality. PCR based screening assay of HMW and LMW glutenin genes showed usefulness in screening of cultivars for good and poor dough quality. Sequencing of HMW-GS Dx5 gene fragment from cultivar GW-273 shows four cystiene amino acids at N-terminal end, which could play major role in determining high elasticity of dough by making disulfide linkage between them and other proteins like LMW-GS and gliadins. Present study may be useful in genetic engineering approaches for developing transgenic wheat with improved dough quality and for the development of export potential.