In order to determine the changes in anthocyanin and flavonoid content in anthers and to identify pollen viability, yellow anther pepper Caya obtained through EMS mutagenesis screening was used as the experimental material with the wild-type Zhangshugang pepper ST-8 as the control. The results showed that the anthocyanin content of the anthers of the mutant Caya was significantly reduced, with no significant change in the flavonoid content and pollen viability. We collected the number of purple anther and yellow anther plants in each population, analyzed the genetic pattern of anther color on the F1 populations obtained between ST-8 and Caya, F2 populations constructed by F1 self-crossing, BC1 population from F1 and Caya backcrossing. The results showed that yellow anthers were controlled by one pair of recessive nuclear genes. Using BSA-Seq method, the genes for color determination located on chromosome 2, between 142 Mbp to 157 Mbp. 9 pairs of SNP markers were designed to genotype the F2 segregating population to further narrow down the candidate region, and the target genes were finally located between 147 461 604 bp and 150 376 942 bp, and two genes closely related to anthocyanin synthesis were screened within the candidate region, namely, Capana02g002586 and Capana02g002763.