Epiphytic orchids comprise 68% of vascular epiphytes on the earth and play an important role in ecological processes in forest canopies. Due to their reliance on specific mycorrhizal fungi for nutrient acquisition, many epiphytic orchids may be endangered and rare. One such rare epiphytic orchid is Phalaenopsis japonica, which is widely used in the floriculture industry. This study aimed to identify the mycorrhizal fungi of P. japonica and determine their roles in seed germination and seedling development. Root samples from 36 adult individuals across four sites in southern Japan were collected, and mycorrhizal fungi were identified using both Sanger and High-throughput Sequencing analyses. The results from both methods revealed adults P. japonica is associated with diverse mycobionts belonging to the Basidiomycota families, Ceratobasidiaceae and Tulasnellaceae. However, two Ceratobasidiaceae OTUs, CE6, and CE22 were dominant. To determine the specific role of the mycorrhizal fungi in P. japonica seed germination and seedling growth, symbiotic cultures were conducted. Seeds inoculated with CE6 showed higher germination percentages and faster protocorm development compared to other fungal strains. Additionally, seedlings inoculated with CE6, CE22, and TU18 displayed varying efficiencies in promoting seedling growth, with CE6 showing the most significant impact. Overall, Ceratobasidiaceae was predominantly associated with seed germination, seedling growth, and the adult stages, while CE6 and CE22 were primary partners throughout the life history of P. japonica. Finally, our findings contribute to elucidating mycorrhizal symbiosis in epiphytic habitats and provide knowledge for the use of such fungal strains in conservation and/or commercial production.