To study on the diversity of endophyte and the antibacterial activity and mechanism of the strains in Emei area of Sichuan Province,and explored the endophytes resources of Coptis chinensis Franch.,identified as 14 species by molecular biology and morphological microscopy,belonged to 2 classes,5 orders,7 families,11 genera.The colonization rates of endophytes in rhizomes,stems,leaves,and fibrous roots were 27.8%,56.7%,52.5%,and 39.6%.Fourteen endophytes from C. chinensis have an antibacterial effect on Staphylococcus aureus,and the diameter of inhibition zone of Cop S01,Cop L01,and Cop FR01 strains is more than 35 mm,the fermentation broth of the three strains of endophytes was found to be effective against S. aureus by diffusion method,and the diameter of the inhibition zone of strain Cop L01 was greater than 20 mm.The minimum inhibitory concentration (MIC) of the fermentation product of this strain was 10 mg/mL,its minimum bactericidal concentration (MBC) was 11 mg/mL.The inhibition mechanism of Cop L01 showed that the product damaged the cell membrane of S. aureus,caused the leakage of intracellular nucleic acid and protein,resulting in the death of S. aureus.This study showed that the endophytes of C. chinensis are rich in diversity,and some strains and their products showed good antibacterial effect on S. aureus.Cop L01 have potential to produce new antibacterial active substances.This provided new strains and ideas for later exploitation of endophyte.