Plants growing in unique habitats and having ethno-medicinal usage among the local ethnic populations of an area are often likely to harbour in them novel endophytic fungi. In the present study five ethno-medicinal plants of the traditionally preserved ‘Sacred forests’ of Meghalaya, India were studied for the presence of fungal endophytes in their roots and stems. Isolation in water agar as per standard procedures and subsequent pure culturing of the fungi in potato dextrose agar medium revealed the presence of a variety of endophytic fungal species. A total of 703 fungal isolates were obtained and classified into 16 taxonomic groups based upon their morphological characteristics. The highest diversity of endophytic fungal taxa was observed for Camellia caduca followed by Schima khasiana, Osbeckia chinensis, Potentilla fulgens and Osbeckia stellata.