This work was devoted to the study of mycobiota of the medicinal plants included in the flora of Azerbaijan, and pathologies caused by the anamorphic fungi. The results demonstrated that the anamorphic mycobiota of the medicinal plants (57 species) in the conditions of Azerbaijan is abundant and various and the mycobiota of the medicinal plants of Azerbaijan consists of 110 species of anamorphic fungi belonging to 22 genera. The most representative genus consisting of 10 and more species in each type are: Septoria – 14, Penicillium – 12, Ascochyta – 11, Fusarium – 10, Aspergillus – 10, other types are represented by 1-8 species. It was also demonstrated that the discovered fungi include the species which cause the different diseases (ascochitosis, septorioz, necrosis, spotting, rubigo, powdery mildew, botritis disease, wilting, phomosis etc.), and the frequency of occurrence of the activators of these pathologies varies greatly within 0.001-17.6%. Among the fungi found on medicinal plants, there are few toxigenic species. The presence of toxigenic fungi and their mycotoxins on the plants used for medicinal purposes is unfavorable and justifies the development of missing or non-existing approaches regulating both the presence of fungi and the quantity of their mycotoxins