To obtain desirable hybrid parents for improving the quality of wheat flour color, 261 wheat cultivar lines from our country’s gene pool were selected as a original population and their genetic polymorphism were analyzed based on molecular markers in wheat genome. A proposed core germplasm group of wheat lines was constructed which included 100 cultivar lines, the proposed core germplasm group was divided into three sub-groups by population genetic structure analysis. The allele diversity at two PPO gene loci were checked in 100 lines of the proposed core gernplasm group , the results showed that the frequencies of Ppo-A1a 、Ppo-A1b、Ppo-D1a and Ppo-D1b were 43%、57%、72%、and 28% in the 100 cultivars lines respectively. The data has supplied a basic information for improvement of wheat PPO activity in the marker-assisted selection.