Endolichenic fungi (ELF) are diverse microbial symbionts that live asymptomatically within lichen thalli. In this study, ELF was investigated from three medicinal lichen hosts namely Cryptothecia scripta, Parmotrema tinctorum, and Dirinnaria applanata from Tippi, Dahung and Dirang. Variations in the occurrence of isolates amongst the sites were determined. A total of 406 fungal isolates were isolated from the surface sterilized lichen fragments. Maximum colonization frequency of endolichenic fungi was observed in P. tinctorum (52.01%), followed by C. scripta (46.01%) and D. applanata (37.3%). The commonly isolated endolichenic fungi belonged to classes Eurotiomycetes, Dothideomycetes, Sordariomycetes and Deuteromycetes. Similarly, common endolichenic fungal genera found associated with the lichen hosts were Aspergillus, Penicillium, Sordaria and Trichoderma. Diversity analyses of endolichenic fungal communities indicated variations in species richness and similarity coefficient. It was observed that diversity was influenced by climatic conditions, altitudinal variations and lichen hosts. Samples collected from Dahung showed higher species richness and greater Shannon weiner's and Simpson diversity indices. Jaccard similarity index of ELF showed similarity of the isolates varied amongst the lichen hosts and in between the collection sites. Almost all the isolates determined for antimicrobial activity showed inhibitory effect against some clinically significant pathogens in varying degree. Amongst the isolates, Trichoderma sp. isolated from all the lichen host showed significant antimicrobial activity against Staphylococcus aureus, Escherichia coli and Candida albicans. The study indicated that lichens harbour diverse ELF with antimicrobial potential. Detailed investigation on their bioactive metabolites might leads to the disvovery of novel antimicrobial drugs.