This study aimed to clarify the genetic mechanisms behind wheat flour color. Flour colorrelated traits (L*, a*, and b*) and polyphenol oxidase (PPO) activity are important parameters that influence the end-use quality of wheat. Dissecting the genetic bases and exploring important chromosomal loci of these traits are extremely important for improving wheat quality. The diverse panel of 205 elite wheat varieties (lines) was genotyped using a highdensity Illumina iSelect 90K single-nucleotide polymorphisms (SNPs) assay to disclose the genetic mechanism of flour color-related traits and PPO activity. In 2 different environments and their mean values (MV), 28, 30, 24, and 12 marker-trait associations (MTAs) were identified for L*, a*, b* traits, and PPO activity, respectively. A single locus could explain from 5.52% to 20.01% of the phenotypic variation for all analyzed traits. Among them, 5 highly significant SNPs (P ≤ 0.0001), 11 stable SNPs (detected in all environments) and 25 multitrait MTAs were identified. Especially, BS00000020_51 showed pleiotropic effects on L*, a*, and b*, and was detected in all environments with the highest phenotypic contribution rates. Furthermore, this SNP was also found to be co-associated with wheat grain hardness, ash content, and pasting temperature of starch in previous studies. The identification of these significantly associated SNPs is helpful in revealing the genetic mechanisms of wheat colorrelated traits, and also provides a reference for follow-up molecular marker-assisted selection in wheat breeding.