Anthocyanins, a major water-soluble pigment in plants, endow horticultural plants with colors and nutritional value, and serve as a key factor in shaping fruit quality and commercial value. Over the past decades, epigenetic modifications have been indicated to significantly influence anthocyanin accumulation and response to various environmental cues. Recently, epigenetic regulation at the population level has become an increasingly important research focus. Here, we briefly describe the recent studies on epigenetic regulation of anthocyanin biosynthesis in horticultural crops, including the repressive role of DNA methylation, the dynamic gene expression control by histone modifications, and gene silencing or regulation mediated by non-coding RNAs. Furthermore, we also discuss recent technological breakthroughs in epigenetic editing and their potential applications in plant breeding. The review aims to provide new, more flexible research perspectives to enhance fruit quality in horticultural crops and to understand the molecular regulation of color formation.