In the last couple of decades, extreme weather events have been increasing, exceeding plants’ tolerance thresholds, and driving mass mortalities in many tree species. Furthermore, many studies suggest that due to their longevity, trees are not able to adapt rapidly enough to keep pace with global climate change. Understanding how trees respond to such weather events and other environmental conditions (such as biotic stress) has thus become crucial for conservation policies and forest management programs. To cope with unpredictable environmental conditions, plants have evolved the ability to alter their physiology, morphology, or development or, in other words, the ability to produce different phenotypes from one genotype. This ability is called phenotypic plasticity, and it plays a major role in plant adaptation. Three factors have been suggested to increase phenotypic variability and thus potentially the resilience of tree populations: intraspecific genetic variability, (micro-)environmental variation, and epigenetic variation. Indeed, a growing body of literature suggests that epigenetic variation might contribute to local adaptation of natural plant populations. Epigenetic mechanisms, such as DNA methylation, can in fact quickly alter phenotypes in response to environmental changes. Variation in DNA methylation can be under genetic control, arise stochastically, or be induced by environmental conditions. Furthermore, phenotypic changes induced by epigenetic variation can be inherited across several generations (especially across clonal generations), suggesting that variation in DNA methylation might contribute to heritable phenotypic variation and, eventually, to adaptation. Although considerable progress has been made in recent years, the link between epigenetic variation and phenotypic variation remains poorly understood.