This chapter explores the interplay between systematics, ecology, and epigenetics in shaping plant evolution and adaptation. First, we highlight the role of epigenetic mechanisms—DNA methylation, histone modifications, and small RNA pathways—in enabling rapid and reversible responses to environmental stress. These processes support both phenotypic plasticity and, in some cases, transgenerational inheritance, providing plants with evolutionary flexibility beyond DNA sequence changes. Second, we examine how epigenetic variation informs taxonomy and phylogenetics. Epigenetic differences can distinguish closely related taxa and reveal ecological divergence even in the absence of significant genetic variation, as shown in mangroves, Spartina, and clonal dandelions. This suggests that epigenetics offers a valuable complementary tool for systematics. Finally, we address epigenetic diversity in agroecosystems, where domestication and monoculture have reduced genetic diversity. Despite this, epigenetic variation persists and contributes to stress tolerance, yield stability, and resilience under agricultural pressures. Advances such as epigenetic markers, epiQTL mapping, and CRISPR/dCas9-based epigenome editing highlight the potential of harnessing epigenetic diversity for sustainable and climate-smart agriculture. In conclusion, epigenetics bridges the gap between ecology, taxonomy, and crop science, offering novel insights into plant evolution and practical pathways for agricultural improvement in the face of global climate challenges.