We test the hypothesis that root microbiomes that establish in Virola surinamensis seedlings vary depending on relatedness to the soil inoculum source and affect seedling growth performance. Abundances of some possibly pathogenic fungi were positively associated with maternal soil and hence candidates for negative effects of growing near a parent tree. Data collected indicates a number of connections between fungal transmission, genotype-specific interactions, and seedling performance that may affect community dynamics of tropical trees.