Endophytes are considered as an important source of bioactive natural products because these microorganisms are able to occupy unique biological niches and grow in non-ordinary environments. Therefore, endophytic fungi of medicinal plants can be developed for medicinal applications. Besides, medicinal properties of plant can be ascribed to its endophytic fungi. Thymus sp. is widely used as a medicinal plant and in this research, the endophytic microflora of this plant was studied. In order to isolate endophytic fungi, 800 segments of 6 Thymus species were collected from its natural habitats in Hamedan province (Iran) and medicinal plants garden during the seasons of spring, summer and fall 2011. Finally, 95 isolates consisting of 11 different fungal genera, 6 yeast isolates and 19 sterile mycelia were obtained. Among the identified isolates, the most abundant genera were Alternaria, Phoma, and Fusarium. The above mentioned genera and the genera Cladosporium and Colletotrichum were first reported from Thymus in Iran. The genera Curvularia, Cylindrocarpon, Drechslera, Aspergillus, Stemphylium and Ulocladium were also, first reported from Thymus in the world.
