To explore the species diversity and ecological functions of endophytic fungi in the roots of Rhododendron simsii Planch under Pinus massoniana forests in central Guizhou, the hairy roots of R. simsii under P. massoniana forests in Wudang (WD), Mengguan (MG) and Longli (LL) areas were collected. DNA of endophytic fungi in the roots was extracted for high throughput sequencing. Alpha was used to analyze the species diversity of fungi. FUNGuild annotation platform was used to analyze the ecological function categories of fungi and explore the core microbial groups in fungal communities.The network graph was used to show the correlation between fungal flora. The results showed that the species diversity of endophytic fungi in the roots of Rhododendron was rich in three regions. The diversity and richness of endophytic fungi of Rhododendron in WD area was the highest. A total of 425799 valid sequences and 817 operational classification units (OTU) were obtained, belonging to 6 phylas, 19 classes, 52 orders, 103 families, and 154 genera. They mainly belong to Ascomycota (81.2%), Zygomycota (5.8%), and Basidiomycota (4.7%). The dominant class, order, and family of them were Eurotiomycetes (43.0%), Eurotiales (39.2%), and Trichocomaceae (39.2%), respectively. At the genus level, Penicillium accounted for the highest proportion (38.60%), followed by Trichoderma (7.20%) and Pestalotiopsis which constituted 6.10%. The fungi in the root had a variety of ecological functional groups, such as Undefined Saprotroph (194 OTU), Plant Pathogen (20 OTU), Soil Saprotroph (18 OTU), Ectomycorrhizal fungi (14 OTU), Lichenized fungi (10 OTU), Ericoid Mycorrhizal fungi (5 OTU), Wood Saprotroph (5 OTU), Arbuscular Mycorrhizal fungi (4 OTU), Endophyte (2 OTU), Animal Pathogen (8 OTU), and 21 kinds of mixed nutritional groups, in which 102 undefined species had no reference in the FUNGuild database. The endophytic fungi in the root can form niche sharing model and have coupling among different functional groups. The expression of core genomes and ecological functional groups formed by fungal groups in key species.