Mycopopulation of yellow gentian growing in plantations was studied in 2008 and 2009. Fourteen species of fungi were registered at seed, out of which five were pathogenic. The most common species was Alternaria alternata (72-74 %). Species of the genus Fusarium (F. oxysporum, F. solani and F. equiseti) were present in a small percentage (2-6 %). These species, as well as F. verticillioides, were isolated from root, and Fusarium sp. was isolated from the flowers. Alternaria alternate, Epicoccum purpurescens, Phoma sp. and Alternaria sp. were regularly present on the leaves and stems.