Wheat cultivar Xiaoyan 6 is an important foundation parent in wheat improvement of China. Ten functional molecular markers including UMN19, UMN25, UMN26, T2, T5, T13, S13, S1, T1, Wx-A1, Wx-B1, Wx-D1, YP7A, YP7B-1, PPO18, and PPO29 were used to identify the composition of genes associated with quality traits in Xiaoyan 6 and its derivatives. Results showed that 78.72% and 82.98% derivatives had the same compositions of genes as Xiaoyan 6 at loci Glu-A1 and Glu-D1 of HMW-GS and locus Wx. Some derivative cultivars had different HMW-GS gene composition, such as Ax2* and Dx5+Dy10, and 25.33% derivatives had the same gene compositions as Xiaoyan 6 at loci Glu-B3 and Glu-D3. Only 17.02% and 38.29% derivative cultivars had the same gene compositions as Xiaoyan 6 at phytoene synthase (PSY) loci Psy-A1 and Psy-B1 and (PPO) gene. The possible reason of the different transmission frequency of these loci in Xiaoyan 6 and its derivatives were discussed.