The present work aimed to study the biodiversity fungal endophytes inhabiting four medicinal plants namely; Cymbopogon citrates L., Thymus vulgaris L., Salvia officinalis L. and Mentha viridis L. collected from Assiut City, Egypt. A total of 15 species and 8 genera were isolated from leaves, stems and roots of the medicinal plants. Fungi were screened for their sensitivity to essential oils extracted from thyme, sage, spearmint and lemongrass. The inhibitory concentration was strain dependant. The majority of fungal strains (74.2%) were inhibited by thyme oil at MICs ranging from 3.125% to 25% (V/V). Some strains of Aspergillus terreus, Botryodiplodia theobromae, Penicillium crustosum and Talaromyces pinophilus were only sensitive to higher concentrations of thyme oil (50% - 100%). In case of saga oil, only 42% of fungal strains were inhibited by low oil concentrations (6.25% - 25%). Oils extracted from spearmint and lemongrass exhibited wide spectrum of inhibitory action at concentrations fluctuating from 3.125% to 25%) and were active against 85% and 90% of the tested fungal strains respectively. ITS sequencing was used to confirm identification of three resistant fungal strains which were diagnosed as Aspergillus terreus AUMC 16070 (GenBank accession no. OQ935432), Lasiodiplodia theobromae AUMC 16098 (OQ930484) and Penicillium crustosum AUMC 16082 (OQ930483).