The material was collected from the section of medicinal plants of the Jagiellonian University Botanical Garden in Kraków. The garden holds a collection of approximately 200 medicinal plant taxa (E. Nowotarska personal communication, 2010). The selection of plant species was done mainly on the basis of their presence in Polish Pharmacopoeia [23], the importance of species for herbal industry (based on the amount Abstract Arbuscular mycorrhizal fungi (AMF) and dark septate endophyte (DSE) associations were studied in 36 medicinal plant species from 33 genera and 17 families, collected from the Botanical Garden of the Jagiellonian University in Kraków. Arbuscular mycorrhiza (AM) was found in 34 species (94%); 26 were of the Arum-type, 4 -Paris and 4 taxa revealed intermediate morphology. The abundance of AMF hyphae in roots varied with particular species, ranging from 2.5% (Helianthus tuberosus) to 77.9% (Convallaria majalis). The mycelium of DSE was observed in 13 plant species (36%), however, the percentage of root colonization by these fungi was low. Spores of 7 AMF species (Glomeromycota) were isolated from trap cultures established from rhizosphere soils of the investigated plants: Archaeospora trappei (Archaeosporaceae), Glomus aureum, Glomus caledonium, Glomus claroideum, Glomus constrictum, Glomus mosseae, Glomus versiforme (Glomeraceae). Our results are the first detailed report of root endophyte associations of the plant species under study. Moreover, the mycorrhizal status of 14 plant species is reported for the first time.