Abstract This study aims to enhance the coloration of pepper fruit by identifying valuable genetic resources through the analysis of single nucleotide polymorphism (SNP). markers and candidate genes associated with fruit pigmentation. Utilizing 197 natural populations of both hot and sweet peppers, we employed specific-locus amplified fragment sequencing (SLAF-seq) to examine 1496 high-quality SNP markers, thereby identifying significant loci contributing to fruit color variation. Our genome-wide association study pinpointed 30 significant SNP sites located on chromosome 6. Further analysis using kompetitive allele-specific PCR(KASP) and phenotypic correlation with fruit color led to the identification of the CA.PGAv.1.6.scaffold919.44 gene, which is implicated in anthocyanin synthesisregulation via the NAC domain, thereby influencing pepper fruit coloration. These findings offer a valuable reference for the advancement of molecular-assisted breeding strategies aimed at improving the fruit color of both sweet and hot peppers.To improve the fruit color of sweet peppers, this study aimed to identify single nucleotide polymorphism (SNP) loci and candidate genes significantly associated with fruit color. A natural population of 197 sweet pepper accessions was used as the material. SLAF-seq was conducted with 1496 high-quality SNP markers to mine excellent variant loci and predict candidate genes. Through Manhattan plot analysis and association analysis with the best linear unbiased prediction (BLUP) values of fruit color, 30 significant loci were detected on chromosome 6. Combining KASP genotyping technology with field phenotypes, the gene CAPGAv.1.6.scaffold919.44 was identified as a candidate gene regulating mature fruit color. It is related to the NAC domain and is hypothesized to alter fruit color by regulating anthocyanin biosynthesis. This study lays the foundation for molecular-assisted breeding of sweet peppers related to fruit color.