Mechanisms responsible for maintaining high diversity of tree species in tropical forests constitute a central question in community ecology. The Janzen-Connell (JC) hypothesis has been invoked for decades to explain the coexistence of large numbers of plant species in natural ecosystems. Briefly, by selectively reducing survival rates of conspecifics occurring near parental trees, natural enemies promote the recruitment of heterospecifics, ultimately increasing species richness at the community level. In Neotropical forests, transplant experiments in which seedlings were grown in soils conditioned by conspecific plant species have shown widespread negative feedback effects and revealed that fungal antagonists of plants might shape population dynamics and promote local biodiversity. While most studies confirming JC effects and looking at plant-fungal interactions have focused primarily on seedlings, seed-infecting fungi that are important candidates for producing strong JC effects are often neglected. To understand how seed survival and germination vary as a function of fungal communities associated with conspecific vs. heterospecific trees, we buried fresh seeds of four species of pioneer trees (Cecropia insignis, C. peltata, C. longipes, Jacaranda copaia) under and away from the crown of 8 adult trees of C. insignis and 4 adult trees of J. copaia at Barro Colorado Island, Panama, and retrieved them after 3 and 12 months of burial. Fresh (not buried) and buried seeds were tested for viability. After surface-sterilization, total genomic DNA was extracted from seeds and sequenced for fungal metabarcoding on the Illumina MiSeq platform. Although the proportion of germinable seeds decreased over time for all species, seed survival varied significantly among species and burial sites. Seed mortality was higher under the crown of conspecifics for J. copaia and C. insignis but did not vary when buried under or away crowns of heterospecifics. We found that all the species differ in their seed-associated fungal communities when exposed to the same soilborne fungi; however, fungal diversity was lower when seeds were buried under the crown of conspecific trees. Our results highlight the importance of seed-fungal interactions and their consequences as driving factors that promote and maintain biodiversity by selectively modulating seed survival.