Dracocephalum moldavica L. which is known as dragonhead is an annual herbaceous aromatic plant belongs to family Lamiaceae. It is native to central Asia and has been naturalized in eastern and central Europe. Extracts and oil from this plant are used widely in the pharmaceutical, cosmetic, food and flavouring industries. Because mycological quality is important for industrial use of seeds of this plant, the goal of the study was to identify the most dominant fungi occurring on Dracocephalum moldavica L. seeds using molecular techniques. The method of molecular identification was based on rDNA-extraction and the subsequent amplification of the D2 large subunit. Two fungal strains (G435/14 and G443/14) were isolated from Dracocephalum moldavica L. seeds. The strains were identified as Fusarium sporotrichioides (G435/14) and Alternaria alternata (G443/14). Most seeds were settling by A. alternata and just few by F. sporotrichioides.