In the present study, the method of tissue culturing was used to isolate the endophytic fungi from healthy ginkgo roots and stems. After repeated separation and purification, 116 Ginkgo endophytes were isolated. Metabolites of these fungi were preliminarily analyzed by high-performance liquid chromatography (HPLC), and a ginkgolide producing endophyte strain was finally screened out. The production of ginkgolides by this strain was more than 11.4 mg/L. The endophytic fungi strain was identified as Mucor spp. by morphology characteristics and phylogenetic analysis of internal transcribed spacer (ITS), and It was the first report in the ginkgolides producing endophytic fungus from Ginkgo biloba.