Gentiana macrophylla is a traditional Chinese medicinal plant. Its dominant active constituents are secoiridoids, mainly gentiopicrin. The objective of this study was to determine whether endophytic fungi isolated from this plant produce the bioactive ingredient gentiopicrin. Primary screening was done by Dragendorff's reaction and the strain re-selection was done with thin-layer chromatography (TLC) and high-performance liquid chromatography (HPLC) to identify the fermentation products of the selected strains. In this study, 20 strains of endophytic fungi were isolated from G. macrophylla, and the extracts from five strains had a positive Dragendorff's reaction. Two strains (QJ16 and QJ18) had a component with the same R(f) value in TLC as that of authentic gentiopicrin and one ingredient of the QJ18 extract had a retention time identical with that of authentic gentiopicrin in HPLC. Therefore, the fungus appears to produce the bioactive ingredient gentiopicrin, as does its host plant, and could be used for the production of gentiopicrin by fermentation.