We studied the biogeography and community structure of root-associated and ectomycorrhizal fungal communities in two related species of tropical Juglandaceae that have disjunct distributions in Asia and Mesoamerica. We tested the effects of environmental and dispersal factors in structuring root-associated fungi at a regional scale. We used Illumina sequencing to document fungi on the roots of Oreomunnea mexicana in Panama and Mexico and Alfaropsis roxburghiana in China. Ectomycorrhizal fungi dominated the communities with both hosts but we detected a more diverse root-associated fungal community in Alfaropsis but higher ectomycorrhizal fungi richness in Oreomunnea. Geographic distance was the best predictor of variation in fungal species composition, when including both hosts and when analyzing each host independently. However, our results showed a high correlation between geographic distance and abiotic variables, and therefore we were not able to determine if the observed changes in fungal community composition were explained also by spatially structured environmental or phylogenetic factors.