Red pigmentation in apple peel significantly contributes to its commercial value, and bagging treatment contributes to enhancing red coloration in fruits. However, the regulatory mechanisms underlying bagging-induced coloration remain largely unexplored. Through bagging treatment, this study aimed to investigate the role of DNA methylation in anthocyanin biosynthesis in the ‘Nagafu No. 2’ cultivar and its bud mutation variant, which has enhanced red coloration. We compared bagging and unbagging treatments in both the bud mutant (Mt-Bagging and Mt-NoBagging) and the wild type (Control-Bagging and Control-NoBagging). Our results demonstrated that bagging significantly promoted anthocyanin accumulation while reducing chlorophyll content. At 30 days post-bag removal, anthocyanin content was highest in the Mt-Bagging group, followed by the Mt-NoBagging, Control-Bagging, and Control-NoBagging groups, and the highest level of redness (a* values) was detected in the Mt-Bagging group. Genome-wide methylation analysis revealed that differentially methylated regions predominantly targeted structural genes within the anthocyanin biosynthesis pathway, including C4H1, C4H3, C4HL, ANS1, and ANS2. Notably, quantitative PCR analysis confirmed that the upregulation of C4HL, C4H3, and ANS1 in the bagged mutant correlated with its intensified red coloration. These findings offer novel insights into the epigenetic regulation of apple peel pigmentation during bagging cultivation.