Members of Thelephora species (basidiomycetes, ectomycorrhizal fungi) are distributed globally, contributing prominently to host tree health and ecosystem stability. But the taxonomical and functional diversity of microbial communities inhabiting in specific niche of such species still remain mysterious. Herein, we employed a comprehensive functional gene microarray (GeoChip 5.0) and amplicon sequencing to explore the taxonomical and functional attributes in different compartments of Thelephora ganbajun - one of the best-known Thelephora species native from southwestern China.