Seed microbial communities are composed of microorganisms vertically transmitted from the mother plant and horizontally transmitted from the surrounding environment during seed development. These microorganisms can have beneficial, neutral or detrimental effects on plant growth, health and fitness, and thus influence plant evolution and ecosystem function. Our aim was to unravel the processes shaping the microbiome of seeds in a foundation tree species, sessile oak (Quercus petraea). We focused on fungi as this group includes phytopathogenic agents known to influence seed survival. Confocal microscopy analyses revealed the presence of fungi in all seed tissues, including the embryo. Metabarcoding data combined with network inference methods showed the presence of plant pathogens, in association with mycoparasites. Seed mycobiota differed among sites with effects of both the elevation and valley but our analyses suggested that site-level abiotic selective pressures shaped the mycobiota in the seed microenvironment, rather than directly filtering the seed mycobiota. Although local adaptation of seed mycobiota was strong, we found significant variations of seed mycobiota richness and composition within populations. These inter-individual differences remained significant after seed fall, despite seed colonization by fungal species originating from the ground. This result indicate that both the environment and the mother tree phenotype structure seed mycobiota. This study sets a basis for future research proceeding along the tree life cycle to identify the seed extended phenotypic traits that control seedling growth and survival across environments.< Réduire