Molecular marker technology has provided a novel and efficient tool for improving qualities in bread wheat. This paper summarizes progress in gene cloning, gene specific marker (functional marker) development and validation, establishment of high-throughput platform in genotyping, as well as integration of molecular marker technology with conventional quality testing and traditional breeding since 2000. Comparative genomic approach was used to discover more than 20 loci controlling important quality traits, and to develop and validate around 66 gene-specific markers for quality traits such as high- and low-molecular-weight glutenin subunits, color associated traits including polyphenol oxidase (PPO) and yellow pigment, as well as starch parameters. Now the availability of reference wheat genome sequence and on-going efforts to sequence diverse wheat cultivars would offer new opportunities to identify loci responsible for various quality traits through improved genome-wide association study (GWAS) and analytical approaches. Development of high-throughput genotyping platform such as SNP arrays, genotyping-by-sequencing and Kompetitive Allele-specific PCR (KASP) have been well-established and will accelerate molecular breeding progress for quality improvement. New cultivars carrying excellent bread-making quality and outstanding agronomic performance such as Zhongmai 1062 and Jimai 23 were developed. Future strategies in using molecular markers in the context of geneediting to fine tune allelic effects are also discussed.