Abstract: In order to identify qualitative markers of a potential mycoherbicide against Canada thistle based on the mycelium of the fungus Stagonospora cirsii VIZR 1.41, changes in its pathogenicity and lipid profiles during submerged cultivation on liquid sucrose-soybean medium were analyzed. The fatty-acid composition of major lipids and the identification of molecular species of structural lipids were determined. The lipid composition during fungal growth changed together with its pathogenicity. The highly pathogenic mycelium of the fungus (at the log phase of growth) was characterized with the relatively highest content of structural lipids: phosphatidylcholine (PC), phosphatidylethanolamine (PE), and ergosterol (ES). Their relative concentration decreased with culture age and a decrease in pathogenicity. The highest lipid yield was found at the beginning of stationary growth phase (at the maximal biomass yield) of S. cirsii; triacylglycerides (TAGs) were the most abundant. The double-bond index of fatty acids in glycerolipids decreased with culture age, and the substitution of molecular PC species (34:2 versus 36:4) and PE (36:4 versus 34:2) was observed as well. High levels of ES, TAG, PC (in particular, 34:2 forms) and PE (36:4 forms) were presumed to be qualitative markers of S. cirsii mycelium.