<p>Epiphytic orchids account for 68% of vascular epiphytes and 69% of orchid species, demonstrating the importance of epiphytism to the diversification of the Orchidaceae. All orchids require mycorrhizal associations with specific fungi at the earliest stages of germination and development, and these symbioses may have played crucial roles in their adaptation to, and diversification within, canopy habitats. We present the first comprehensive comparison of fungal communities, encompassing both epiphytic and terrestrial orchids as well as their habitat substrates (bark and soil) on Yakushima Island, Japan. We analyzed mycorrhizal communities associated with 29 orchid species, representing eight tribes in four subfamilies, using both Sanger and high-throughput sequencing (HTS) methods, and also characterized fungal communities in the substrates using HTS. Our results reveal that epiphytic and terrestrial orchids have differing mycorrhizal communities and the fungal composition of their habitat substrates also differs. Although overall fungal richness was lower in epiphytic than in terrestrial substrates, the diversity of fungi in the rhizoctonia, including members of Tulasnellaceae, Ceratobasidiaceae, and Serendipitaceae, was similarly high for both habitat types. Furthermore, some rhizoctonia fungi were shared between orchid life forms and exhibited symbiotic compatibility across habitats in in vitro culture. Although rhizoctonia communities differed between habitat substrates, comparable diversity and the presence of shared taxa across habitats imply that these fungi may have reduced barriers to canopy colonization and contribute to the successful establishment and diversification of epiphytic orchids.</p>