Abstract:Objective: To isolate the endophytic fungi from Cephalotaxus fortunei and investigate their antimicrobial activities. Method: Endophytic fungi were isolated by tissue-culture method and antimicrobial activities of endophytic fungi were investigated by using filter paper method and the active strains were preliminarily identified by morphological and molecular method. Result: Thirty strains of endophytic fungi were isolated from the roots, stems and leaves of wild C. fortunei in Qinba mountain. 20 strains (66.67%) showed antimicrobial activity against one or more of the tested microbes, and the strain CFEF013 has strong inhibition activity to all target strains. By morphological and molecular identification, 7 strains with strong antimicrobial activity were classified into genera of Fusarium (4 strains), Cytospora (1 strains), Pestalotiopsis (1 strain) and Mucor (1 strain). Conclusion: There are multiple endophytic fungi in C. fortunei, and their metabolites have good antimicrobial activities.