Huperzine A is isolated from Huperzia serrata and is used for treatment of Alzheimer's disease, due to its low toxicity and long effective period. The decrease in H. serrata sources means that natural huperzine A cannot meet the needs of clinical therapy. In this study, >200 endophytic fungal strains were isolated from H. serrata, and screened using high-performance liquid chromatography. Strain ES026 produced huperzine A. Production was identified and quantified by liquid chromatography-tandem mass spectrometry, and the yield of huperzine A was 1 μg/g dried mycelium. ES026 strain was identified as Colletotrichum gloeosporioides by morphology, polymerase chain reaction with species-specific primers and rDNA internal transcribed spacer sequence. ES026 contributes to the breeding of cultivated strains with high yield of huperzine A. Meanwhile, the strain was suitable for the study of biosynthesis of huperzine A.