Ectomycorrhizae is a symbiosis established between tree roots and soil-borne fungi. Intrinsic to temperate and boreal forest ecosystems, ectomycorrhizal symbiosis is critical for tree nutrition, especially water uptake, also affecting the capacity of trees to adapt to their environment. Our understanding of the establishment and modulation of this symbiotic process is still in its infancy and, until now, the possibility of epigenetic regulation remained unexplored.