Abstract: The species, distribution and diversity of endophytic fungi in Alternanthera philoxeroides plants were studied by sampling, tissue isolation, culture and identification. The results showed that the species of endophytic fungi in Alternanthera philoxeroides plants were rich, and total of 16 endophytic fungi were isolated from the stems and leaves. Among them, 15 species belonging to 12 genera were sporulation fungi and 1 species were non sporulation fungi. The sporulation fungi were belonging to Deuteromycete. The Aspergillus sp.1, Aspergillus sp.2, Colletotrichum sp., Macrophoma sp., and Curvularia sp. were dominant species of endophytic fungi from Alternanthera philoxeroides plants.These fungi were distributed in all tissues tested and the isolation rate of these fungi was high. It was also showed that the endophytic fungi of Alternanthera philoxeroides were widely distributed in various tissues.Their total colonization rate was 81.5%. The fungus colonization rate in old stem tissue was highest and it was 90.9%. Habitat and tissue types had important effects on the community structure of Alternanthera philoxeroides endophytic fungi and their colonization rate.