Abstract: 【Objective】The aim of this study was to investigate the biological diversity and antimicrobial activities of endophytic fungi of Pterocarpus santanilus, providing reference for new antimicrobial active substances.【Method】Samples of roots, stems and leaves of three healthy P.santanilus plants were collected from the Chinese Medicine Garden of Guangdong Pharmaceutical University in Guangzhou.The endophytic fungi of P.santanilus were isolated by tissue block isolation method and were identified by morphological and molecular biological methods.The antimicrobial activities of endophytic fungi fermentation broth against Staphylococcus aureus CMCC26003, Escherichia coli CMCC44102, Shigella dysenteriae CMCC51252, Salmonella typhimurium CMCC50115, Candida albicans ATCC10231 and Aspergillus niger CMCC98003 were studied by the paper disk diffusion method and mycelium growth rate method respectively.【Result】A total of 337 endophytic fungi were isolated from 450 P.santanilus tissues(172 in leaves, 66 in stems and 99 in roots), belonging to 15 genera.The relative isolation rate and colonization rate of endophytic fungi in leaves were the highest, they were both 79.63%.The diversity index of endophytic fungi in leaves, stems and roots were 1.02, 0.93 and 0.64 respectively, and there was significant difference among them(P< 0.05).Trichoderma sp.genus was the dominant genus in root, and the relative isolation rate was 28.28%.Penicillium sp.genus was the dominant endophytic fungi genus of stems and leaves, and the relative isolation rates were 46.97% and 52.91% respectively.The results of the antimicrobial activities of the 45 endophytic fungi fermentation broth from P.santanilus showed that 16 strains(35.56%) had the antibacterial activity against E.coli CMCC44102, S.aureus CMCC26003, S.typhimurium CMCC50115 and S.dysenteriae CMCC51252;36 strains(80.00%) showed the inhibition activity against C.albicans ATCC10231and A.niger CMCC98003.And 15 strains(33.33%) could inhibit the growth of all the six pathogens.L9(Colletotrichum sp.) showed the best antimicrobial activities.It had an inhibitory activity of 67.35% against A.niger CMCC98003 and the diameter of inhibition zones against the other five pathogens were all more than 10 mm.【Conclusion】Theendophytic fungi communityin P.santanilus istissue specific, and the species diversity of P.santanilus endophytic fungi is rich, and there is a high proportion of endophytic fungi with good antibacterial and antifungal activities.The endophytic fungi of P.santanilus provide strain resources for screening and development of new antimicrobial active substances.