Abstract: In order to know the community and ecological distribution of endophytic fungi in Metasequoia glyptostroboides, the community structure and ecological distribution of endophytic fungi in Metasequoia glyptostroboides grown in Xinyang were studied by sampling, isolating and identifying. The result showed that the biological diversity of the endophytic fungi was rich. Twenty five fungi were obtained in this study. Among them, twenty sporulated fungal species belonged to deuteromycetes and other species were non-sporulated fungi. The study also showed that Phomopsis sp., Alternaria sp.,Colletotrichum sp. and Macrophoma sp. were dominant fungi. The endophytic fungi could be isolated in every tested plant parts of Metasequoia glyptostroboides and their colonization rate was 53.5%. Habitat and tissue type of the plants were main factors that affected the biological diversity and community of the endophytic fungi mostly. The study could provide basic data for studying and using of endophytic fungi.