Endophytic fungi are an underexploited resource of natural products and have a capacity to produce diverse classes of plant-derived secondary metabolites. Here, we investigated the diversity of endophytic fungi from Huperzia serrata and the potential for discovering novel fungal natural products. One hundred and fifty-five endophytic fungi isolates obtained from H. serrata, belonging to four classes Dothideomycetes (47.3 %), Sordariomycetes (36.8 %), Eurotiomycetes (10.6 %) and an undefined class (5.3 %, Mucoraceae), were grouped into nine genera based on morphological and molecular identification. Colletotrichum, Cladosporium, Sordariomycetes and Guignardia were the dominant genera, whereas the remaining genera were infrequent groups. To our knowledge, the fungal genera Mucor and Neurospora were first reported in Huperzia plant. Among these endophytic fungi isolates, strain B14, belonging to Penicillium oxalicum, gave a gray precipitate with Dragendorff's reagent. A new pentapeptide was isolated from the culture of strain B14, and its chemical structure was elucidated on the basis of spectroscopic data from (1)H NMR, (13)C NMR and ESI-MS/MS. Taken together, H. serrata has a significant diversity of endophytic fungi that could be a rich resource for the discovery of new natural products.