High molecular weight glutenin subunits (HMW-GS), 1B·1R translocation, polyphenol oxidase (PPO) activities, and yellow pigment content are mostly correlated with the processing quality of common wheat (Triticum aestivum L.). An accurate and fast characterization of these genes is of great importance in the improvement of wheat quality. In this study, a total of 321 wheat genotypes, including 100 Xinjiang local wheat cultivars, 130 introductions from other provinces of China and 91 introductions from other countries, were analyzed by SDS-PAGE method. In addition, the functional markers of Dx5, Bx7, By8, By9,1B·1R, PPO16, PPO18, PPO29, and YP7A were used to detect their allelic variations. Twenty-one subunit combinations were found according to the SDS-PAGE data, 3 types at Glu-A1 locus with Null as a major subunit, 10 types at Glu-B1 locus with Bx7+By8 and Bx7+By9 as major subunits, and 8 types at Glu-D1 locus with Dx2+Dy12 and Dx5+Dy10 as major subunits. The frequencies of the Dx5, Bx7, By8, and Bx9 subunits revealed by functional markers were 38.3%, 85.7%, 38.9%, and 42.7%, respectively, with 97.2%, 98.4%, 93.4%, and 97.2% of consistency with SDS-PAGE results, respectively. Eighty-six genotypes had 1B·1R translocations, with 22.0% in Xinjiang local cultivars, 31.5% in the introductions from other provinces of China, and 25.0% in those from other countries, respectively. The frequencies of Psy-A1b detected by YP7A marker were 9.0%, 10.8%, and 5.4% among three group genotypes, respectively. The PPO18 marker for the Ppo-A1 locus yielded Ppo-A1b allele with frequencies of 38.0%, 43.8%, and 45.7% among three group genotypes, respectively. The Ppo-D1a allele frequencies were 48.0%, 66.9%, and 40.2% among three group genotypes, respectively, according to the PPO16 and PPO29 markers at Ppo-D1 locus. However, only 74 genotypes contained Ppo-A1b and Ppo-D1a alleles at both loci, accounting for 23.0% of the genotypes. The functional markers applied in this study were repeatable, accurate and stable, and can be effectively used in wheat quality breeding.