Endophytes induced the biosynthesis or accumulation of the active components of the host medicinal plants,making the production and distribution of these active components different in species,organs,tissues and growth stages. F. hupehensis was a geo-authentic crude drug in Enshi area with a long medicinal history. Peiminine B was the main active component in F. hupehensis,with its functions of anti-colonic cancer,relieving myocarditis,alleviating lung injury and etc.We use gas chromatography (GC) to determine the content of peiminine B in bulbs,flowers and leaves of F. hupehensis to explore the content of peiminine B,the composition of endophytes and the antibacterial activity of its secondary metabolites in different tissues of F. hupehensis. The 16S rDNA and ITS sequencing were used to identify the species of endophytic bacteria or fungi,respectively. The agar diffusion method and double dilution method were used to study the antibacterial activity of secondary metabolites of endophytes against 10 strains of bacteria tested. The results showed that the content of peiminine B in leaves of F. hupehensis was the highest with (3.99±0.10) mg/g,which was 1.78 and 4.24 times as much as that in bulb and flower,respectively. Four strains of endophytes were isolated from F. hupehensis,identified as Pseudomonassp. BM-X-6,Arthriniumsp. BM-Z-5,Aspergillus sp. BM-Z-1 and Aspergillus sp. BM-Z-3. The secondary metabolites of three endophytic fungi had stronger antibacterial activity than Pseudomonas sp.BM-X-6. Meanwhile Arthriniumsp. BM-Z-5 had the broadest antibacterial spectrum,which showed moderate antibacterial activities against Klebsiella pneumoniae,Staphylococcus aureus,Micrococcus luteus,Acinetobacter baumannii and methicillinresistant Staphylococcus aureus(MRSA). It will provide a reference for expanding the medicinal parts and effectively saving resources of F. hupehensis and will provide a novel way to alleviate bacterial resistance and develop new antibacterial drugs.