The choice of host plant is of critical importance when working with endophytic fungi. The exploration of endophytic fungi is still an emerging field and all plants seem to harbour fungi with some bioactive content and activities. However, there are certain metabolites that are characteristic of certain biotopes. Thus, a rationale for selecting promising plant sources should be established. Of particular interest are the plants that are used as medicinal plants or plants that populate a unique environment. Artemisia is a widely used medicinal plant. In this research work, the endophytic mycota of Artemisia scoparia was studied. In order to isolate endophytic fungi, 155 plant segments from 20 samples of Artemisia scoparia were collected from its natural habitat in Dachigam National. This habitat is a unique environment and a protected area. Six different fungal isolates were obtained from root, leaf and stem plant parts. Among the identified isolates, the most abundant genera were Gliocladium solani followed by Penicillium melinii with a colonization frequency of 62 and 37.5% respectively. The objective of this study was to report new data regarding the endophytic fungi found in medicinal plant Artemisia scoparia. This systematic investigation revealed that traditional medicinal plants are a rich and reliable source of novel endophytic fungi.