Mycorrhizal fungi are important factors driving niche partitioning in terrestrial orchids and may contribute to orchid coexistence. However, little is known about the mycorrhizal communities associated with sister taxa that occupy similar habitats, and even less is known about the changes in their fungal community composition over seasonal and annual cycles. Over a three-year period, this study assessed the root mycorrhizal fungi of two coexisting congeneric species: Paphiopedilum dianthum and Paphiopedilum hirsutissimum using high-throughput sequencing to determine whether their fungal community and functional composition is determined by annual and seasonal variation, or the host species specificity. The results show that: 1) the fungal communities of the two orchid species were generally similar and belonged mainly to the phylum Ascomycota (77%), of which 30% were from the class Sordariomycetes, followed by 18% belonging to Dothideomycetes; 2). P. dianthum roots had a higher mycorrhiza alpha diversity compared to P. hirsutissimum, but not in all seasons; and that 3). The fungal communities of P. hirsutissimum were more sensitive to seasonal changes compared to P. dianthum. These results could provide a theoretical basis for the use of mycorrhizal technology as a foundation to restore the wild Paphiopedilum, and underpin further exploration of the relationship between the community structure of orchid endophytic mycorrhizal fungi and their temporal ecological function.