How perennial organisms adapt to environments is a key question in biology. To address this question, we investigated ten natural black poplar ( Populus nigra ) populations from Western Europe, a keystone forest tree of riparian ecosystems. We assessed the role of (epi)genetic regulation in driving tree species evolution and adaptation over several millions of years (macro-evolution) up to a few generations (micro-evolution). At the macro-evolution scale, polar experienced differential structural (gene loss) and regulation (expression and methylation) reprogramming between sister genomic compartments inherited from polyploidization events. More interestingly, at the micro-evolution scale, both genetic and epigenetic variations differentiate populations from different geographic origins, targeting specifically genes involved in disease resistance, immune response, hormonal and stress response that can be considered as key functions of local adaptation of long lifespan species. Moreover, genes involved in cambium formation, an important functional trait for forest trees, as well as basal functions for cell survival are constitutively expressed though methylation control. These results highlight DNA methylation as a marker of population differentiation, evolutionary adaptation to diverse ecological environments and ultimately opening the need to take epigenetic marks into account in breeding strategies, especially for woody plants.Read less <