To ensure long-term survival of epiphytic orchids through active reintroduction, more research on critical life cycle stages such as seed germination and seedling establishment are needed. In this study, we used in vitro germination experiments to investigate the role of mycorrhizal fungi in determining seed germination and growth in the endangered epiphytic orchid species, Dendrobium chrysotoxum. Symbiotic seed germination experiments were conducted for 90 days under different light conditions with fungal strains isolated from protocorms of D. chrysotoxum and three sister species. Molecular analyses showed that five strains belonged to the typical orchid mycorrhizal family Tulasnellaceae, whereas the other two strains belonged to the Sebacinaceae and the genus Coprinellus. Fungal inoculation, light conditions, and their interaction had a significant effect on protocorm formation and seedling development. Three fungal isolates, including two from D. chrysotoxum and one from D. catenatum, significantly stimulated protocorm formation and seedling development under light conditions. However, fungi isolated from host protocorms (GC-14 and GC-15) produced the highest number of seedlings after 50 days (49.5 ± 8.5%, 51.3 ± 9.0%, respectively), while the fungus isolated from D. catenatum protocorms produced the maximum number of seedlings only after 90 days (48.7 ± 16.1%). To conclude, this study has shown that light conditions and the identity of fungi had a strong effect on in vitro seed germination and seedling formation in an epiphytic orchid, with fungi isolated from host protocorms leading to accelerated germination and seedling formation. Therefore, fungal source should be taken into account when using seeds and compatible fungi for seedling propagation and in situ reintroduction.