New DNA sequencing technology is driving advances in wheat genomics that are providing new opportunities to improve wheat quality. Reference genome sequence data and low-cost sequencing are making the association of quality traits with specific genes and alleles possible. This information, in turn, is providing tools for quality selection in wheat breeding by removing a major constraint to the rapid development of varieties and enabling increased wheat productivity. New approaches to varietal identification are likely to emerge with the ability to analyze complex mixtures. Development of improved wheat milling and end-product processing will also be enabled by a greater understanding of the genetic and molecular bases of processing performance. Analysis of expressed genes (transcriptome) in the developing wheat seed is providing new insights into the molecular basis of grain formation and wheat quality as well.