Objective: To select alkaloid-producing endophytic fungi strains from Fritillaria anhuiensis. Methods: The endophytic fungi were selected from the bulbus of Fritillaria anhuiensis, by tissue explants, thin layer chromatography, the high performance liquid chromatography and high performance liquid chromatography-evaporative light scattering detection, morphologic observation and molecular biological methods. Results: One strain as an endophytic fungi capable of producing alkaloid was selected from the bulbus of Fritillaria anhuiensis, and was classified as Alternaria tenuissima. Conclusion: The selected alkaloid-producing endophytic fungi strain bm-2 from Fritillaria anhuiensis provide theoretical foundation for solving the problem of the deficient medical resources of Fritillaria anhuiensis.