The biotic and abiotic environmental experience of plants can influence the offspring without any changes in DNA sequence. These effects can modulate the development of the progeny and its interaction with micro-organisms. This interaction includes fungal endophytic communities which have significant effects on trees and their associated ecosystems. We highlight potential maternal mechanisms through which endophytes could influence the progeny. We argue that a better understanding of these interactions might help predict the response of trees to stress conditions and to enhance the efficiency of tree breeding programs.