As an important agronomic trait of pepper， fruit color directly affects the commercial value of pepper， and the analysis of its genetic mechanism can provide guidance for the improvement of pepper fruit appearance quality. In this study， the genome-wide association study （GWAS） was used to identify SNPs and candidate genes that significantly associated with the fruit color in pepper. By taking the natural population composed of 195 annual peppers， the fruit color including immature fruit color and mature fruit color were investigated in two calendar years （2020 and 2021）. Through the DNA sequencing and SNP variation detection， the high-quality SNPs filtrated by quality control were used for GWAS. The results showed that the phenotypes at pepper fruit color traits collected from the two calendar years were completely consistent， indicating the inheritance of the traits. The frequency distribution of green fruit color and bright red fruit color was the highest， up to 89.74% and 60.51%， respectively. GWAS analysis revealed eight SNPs associating with the pepper fruit color， these loci were distributed on four chromosomes 0， 1， 3 and 4. LD block analysis was performed on significant SNP sites and candidate genes were screened， enabling the annotation of 31 candidate genes. It includes several strong candidates including the respiratory burst oxidase homologous protein A （capana01g000138）， isoflavone 2' - hydroxylase-like （capana04g000616， capana04g000617， capana04g000618， capana04g000619， capana04g000620， capana04g000621 and capana04g000622） and F-box-like/WD repeat-containing protein TBL1Y-like （Capana04g000624）. These results will provide a reference for molecular assisted breeding of fruit color in pepper.