Zanthoxylum oxyphyllum Edgew. is a medicinal plant widely been used by the local tribal communities of Assam as an alternative source of medicine for the treatment of various diseases. In the present study, endophytic fungi associated with Z. oxyphyllum were undertaken with an aim to investigate the isolates for their antimicrobial potential. The endophytic fungi were recovered using four different media, namely, Malt Extract Agar (MEA) media, Potato Dextrose Agar (PDA) media, Water Agar (WA) media and media amended with the Plant Extract (PEA) from samples collected from three sites. Altogether, 18 isolates of endophytic fungi were isolated from 150 surface sterilized and healthy leaf fragments. Colletotrichum was found to be dominant endophytic genus with 7 different species. Other isolated endophytic fungal genera were Fusarium, Curvularia, Aspergillus, Corynespora and isolates belonging non-sporulating fungi categorised as Mycelia Sterilia. The endophytic fungi were determined for antimicrobial activity against selected clinically significant human pathogenic test organisms. Ethyl acetate crude extracts of all endophytic fungi exhibited antimicrobial activity by inhibiting a minimum of one of the four test pathogens. Amongst the isolates, crude extracts obtained from Fusarium sp. and five Colletotrichum spp. showed wide-spectrum antimicrobial activity against all the test organisms. The study indicated that Z. oxyphyllum harbours a wide range of endophytes capable of producing secondary metabolites with antimicrobial properties. Further detailed investigation of their bioactive metabolites might lead to discovery of compounds with potential therapeutic applications as a new source of medicine.