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Nepeta rtanjensis(Lamiaceae) is an endemic and critically endangered plant species that grows only on Rtanj Mountain in the southeastern Serbia. Due to its endemic character and distribution separated from the other Nepetaspecies in Mediterranean Basin, N. rtanjensishas been considered as a relict. It has been noticed that number of individual plants in natural habitat rapidly decreases. Hence, the project of reintroduction of this plant was successfully conducted. However, many aspects of its biology still remain unknown and necessary to investigate. In that sense, epiphytic and endophytic Nepeta rtanjensisphyllosphere fungi were studied at three sites in Serbia: Javor—Locus classicus, with autochthonous population and with reintroduced plants, and Belgrade with micropropagated specimens in experimental field. The sites in Javor are located in the area of the Mountain Rtanj. From both, the surface and the interior of leaves, a total of 49 taxa of microfungi were identified, belonging to 35 genera. Alternariaspp. was reported on all studied sites with the highest isolation frequency (>75 %). Similarity between epiphytic and endophytic fungal assemblage was moderate. The highest fungal diversity was detected on site with the autochthonous Nepeta rtanjensispopulation. Phyllosphere mycobiota show the presence of a large number of viable propagules, with a low frequency of occurrence of symptoms, due to the specific anatomy of the leaf and a well-developed indumentum.