In order to reserve the resource of Ginkgo biloba L. and to seek for alternatives of flavonoids, the flavonoid- producing endophytes were isolated and selected from the root, stem and leaf samples of Ginkgo biloba. Firstly, endophytic fungus was obtained through the PDA and Martin medium. Secondly, their diversities were analyzed. Thirdly, whether these strains could yield flavonoid were tested by the ways of characteristic color reaction of flavonoid, thin layer chromatography (TLC) and High Performance Liquid Chromatography (HPLC). In the end, the production of flavonoids was measured by UV-spectrophotometry, and these strains according to the morphological characteristic and the similarity of the nucleotide sequence of internal transcribed spacer (ITS) between rDNAs were identified. The results showed that 217 strains were isolated from the samples, which were classified into 8 orders, 10 families and 13 genera by morphological study. Among the strains, the strains named GF111 and GF521 were proved to produce flavonoids. The amounts of total flavonoids in GF111 and GF521 were (14.50 ± 1.30) mg/L and (21.10 ± 1.30) mg/L, respectively. The strains named GF111 and GF521 were classified as Mucor circinelloides and Fusarium oxysporum. The results indicated the distribution of the endophytic fungi varied with different parts of Ginkgo biloba. The strains named GF111 and GF521 had a higher production of flavonoids, so these strains could be used as the alternative fungus for bio-fermentation of flavonoids.