The bread-making quality of wheat is strongly influenced by prolamins, mainly composed of glutenins and gliadins. Prolamin genes belong to complicated multi-gene families, the genomic organization and evolution mechanism of them are still unclear. To study the structural organization and molecular evolution of these gene families, we sequenced and analyzed three tightly linked loci: Glu-D3, Gli-D1 and Gli-D3, which were mapped on the short arm of group 1 chromosome and encoded LMW-glutenins, gamma-gliadins and omega-gliadins, respectively. Eighty BACs from six contigs were selected based on BAC library screen and physical map of Ae.tauschii, generated totally 8Mb sequences. Illegitimate recombination and double-strand break repair mechanisms play a major role in the genomic evolution. This study provides insights into understanding the prolamin genes genomic structure and evolution, that will be helpful to study the evolution mechanism of wheat genome and contribute to the wheat breeding.