To study the diversity, distribution and community structure of endophytic fungi, a medicinal plant Cinnamomum camphora (L.) Presl., was selected from ayurvedic garden of Banaras Hindu University (BHU), Varanasi, India. Differences were observed between the endophytic myco-population of young and mature tissues of leaf, stem and petiole. The leaf segments with midrib (43.93 %, Isolation Frequency) were found to have more endophytic isolates than the vein less foliar segments (21.21 %), however, the segments with lateral veins (34.84 %) are comparatively closer to the midrib segments in endophytic recovery. The mature tissues are found to harbor more endophytic diversity than the young ones. It was observed that some endophytes restrict the probable invasion of other endophytes in their respective tissues, and thus defend their tissue specificity. The endophytic microbes obtained in this study are evaluated for their antimicrobial activity, against an array of human and plant pathogens. Pestalotiopsis sp. showed significant inhibitory activity against Phytophthora cryptogea (57.7 %), Pythium aphanidermatum (54.5 %) and Microsporum nanum (51.4), while Phomopsis sp. inhibited P. aphanidermatum moderately. This preliminary work not only resolutes the understanding about plant-endophytes interactions and distribution within the host, but also provides platform for screening and isolation of novel natural antimicrobial compounds, that may be utilized in designing novel drugs for sustainable relief to the mankind.