Epigenetic modifications, such as DNA methylation, histone modifications, chromatin remodeling, and RNA-associated silencing, play critical roles in regulating gene expression without altering the DNA sequence. In horticultural crops, these mechanisms control key biological processes, including fruit development and ripening, flowering time, stress adaptation, and phenotypic plasticity. Driven by high-throughput sequencing and multi-omics technologies, researchers have begun to uncover the dynamic landscape of plant epigenomes. Notably, the Encyclopedia of DNA Elements (ENCODE) project was developed to systematically map functional elements within the genome. Inspired by this initiative, similar strategies have been increasingly applied to plants to identify regulatory elements, chromatin states, and transcriptional networks. This review integrates recent findings on epigenetic regulation in model and horticultural species, emphasizing the role of epigenomic tools and ENCODE-like approaches in annotating cis-regulatory elements, epigenetic markers, and long non-coding RNAs (lncRNAs). We discuss how epigenetic modifications mediate developmental transitions and responses to environmental cues. Finally, we propose a framework for integrating ENCODE-derived insights with precision breeding to improve yield, quality, and stress resilience in horticultural crops. These advancements offer exciting opportunities for translating epigenomic knowledge into practical crop improvement strategies.

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