Ginkgo biloba, as a tree (medicinal plant), contains a complex assemblage of endophytic fungi that can fluctuate temporally. The temporal variation of endophytic fungi in this tree could affect bioactive compounds that are potentially useful for agricultural applications. Generally, perennial plants as Ginkgo biloba are more suitable for many fungal species and the potential exists for the plant-fungal interaction. These fungal species are living in intercellular spaces among plant tissues, and this interaction between fungi and plants does not cause any visible damage to plant tissues. Some fungal species are more dominant endophytes in ginkgo trees that included Alternaria, Colletotrichum, Phoma, Fusarium, Cladosporium, Pestalotiopsis, Phomopsis sp., Phyllosticta sp., and Peyronellaea. The interaction of endophyte fungi and tree of Ginkgo biloba could enhance the defenses and growth of plant, with changing levels of secondary metabolites. Therefore, endophytic fungi are concentrated in some parts of the Ginkgo biloba and contain high fungal diversity.