Objective To select the strains which can produce tanshinone ⅡA like its host plant Salvia miltiorrhiza bung. Methods A total of 50 strains of endophytic fungi were isolated from healthy, living and symptomless tissues of Salvia miltiorrhiza bung, among which 29 strains were obtained from the root, 14 from the stem, 3 from the leaf, 3 from the flower and 1 from the seed. Their antimicrobial activities against nine different bacteria, including both Gram-negative and Gram-positive bacteria, were measured by Oxford plate agar diffusion bioassay. Results Our data showed that all but four strains had significant antibacterial activities on at least one indicator bacterium to some extent, and five strains (DR1, DR4, DR16, DR18 and DF2) manifested quite prominent antibacterial activities against certain pathogenic bacteria. In some degree, it might indicate that this endophytic fungus isolated from the tissues of Salvia miltiorrhiza bung has a potential value as a natural antibacterial medicine as well. Thin layer chromatography (TLC) and high-performance liquid chromatography (HPLC) were carried out to test selected strains, both inside and outside of the cell to see if any strain can produce tanshinone ⅡA. The result showed that extracts from three strains, labeled as DR12 (outside cell), DR21 (inside cell) and DF3 (inside cell), had a component with the same Rf value in TLC assay as that of authentic tanshinone ⅡA. The extract from DR12 (outside cell) and DR21 (inside cell) had a peak at retention time identical to that of authentic tanshinone ⅡA in HPLC. Conclusion The fungi appear to produce the bioactive compound tanshinone ⅡA, and they could be used to produce tanshinone ⅡA by fermentation. It provides a new way to synthesize this natural medicine.