The study of Endophytic fungi in the medicinal plants showed quite a variation. The plant Ocimum sanctum showed six types of fungi Trichoderma viridae, Fusarium solani, Gliocladium roseum, Cladosporium sp., Cladorrhinium sp. and Nigrospora sp. that were isolated from rhizosphere and found to be 42.8 % of the population of total fungi isolated, while only one type of endophyte, Mycelia sterilia was 14.2% of the total population of the isolates. The four fungi Fusarium solani, Gliocladium roseum, Mycelia sterilia and Nigrospora sp. were isolated as endophytes. with 42.8% of the total population of the isolates. In the plant Santalum album five fungi Trichoderma viridae, Stachylidium extorre, Pseudobotrytis sp., Fusarium oxysporum, Mycelia sterilia, were isolated from rhizosphere and found to be 55.55% of the population of total fungi isolated. While four fungi Chalaropsis sp., Phoma glomerata, Collectotrichum sp. and Fusarium solani were isolated as endophytes which accounted for 33.33%. The fungi common both as rhizospheric and endophytic include one isolate Collectotrichum sp. with 11.11% of the total population of the isolates. The presence of vesicles was observed within the cortical cells of both the plants Ocimum sanctum and Santalum album.