DNA methylation plays an important role in mediating the phenotypic variations observed in many traits and plants. In this study, we explored the origin of berry flesh color at the metabolic, transcriptional, and epigenetic levels. To this end, a comprehensive multiomics analysis of grape (Vitis vinifera L.) berry flesh was carried out in an F₁ breeding population segregating for white- and red-fleshed siblings. The results showed that differences in DNA methylation levels at the MYBA1 promoter could effectively distinguish the white- and red-fleshed varieties. More precisely, an approximately 1-kb region in the MYBA1 promoter was hypermethylated in white-fleshed genotypes compared with the red-fleshed genotypes. This variation in methylation level was consistent among leaves, berry skin, and flesh for a given genotype, and was inherited by the F₁ generation arising from crosses between parents with different phenotypes. A targeted increase in the DNA methylation levels in the MYBA1 promoter led to decreased MYBA1 expression and anthocyanin levels in transgenic grapevine hairy roots, indicating that anthocyanin biosynthesis is modulated by differential methylation at this locus. Taken together, these results suggest that the variation in methylation at the MYBA1 promoter is stable, heritable and co-segregates with grape flesh color, providing a pertinent epiallelic variation that could be used as a breeding marker to select for grape flesh color. Our findings also offer insights into the mechanisms regulating anthocyanin accumulation in grape flesh.