Aims: The main objective of the present study was to study the diversity of endophytic fungi from Ruta graveolens, an important medicinal plant. The alkaloids produced by this plant have been used in many medical applications. The endophytic fungi that inhabit the plants are also recognized as rich sources of secondary metabolites. This study was aimed to isolate, identify and study the diversity of endophytic fungi in R. graveolens and to screen the isolates for their antimicrobial activities. Methodology and results : A total of 12 different fungal genera were isolated from R. graveolens collected from various sites in and around Bangalore. The species richness and colonizing frequency of endophytic fungi in this plant are comparatively less than other plants. This may be due to the secretion of the plant's phytochemicals, as it has antimicrobial activity and more than 120 phytochemicals in it. Screening of antimicrobial activity of all 10 isolates was done by agar well diffusion method, of which 80% of the fungal isolates could produce antimicrobials. Conclusion, significance and impact of study To conclude R. graveolens being a good medicinal plant along with its rich source of endophytes and their medicinal properties, can be exploited for the therapeutic applications.