Stagonospora cirsii Davis, a fungal pathogen isolated from Cirsium arvense (commonly called Canada thistle) and proposed as a potential mycoherbicide of this perennial noxious weed, produces phytotoxic metabolites in liquid and solid cultures. Stagonolide, the main phytotoxic metabolite, and five new related nonenolides, named stagonolides B-F, were isolated from the fungus. When grown on solid culture, nonenolide yields increased. A further four nonenolides were isolated and characterized by spectroscopy. Three were new compounds and named stagonolides G-I, and the fourth was identified as modiolide A, previously isolated from Paraphaeosphaeria sp., a fungus separated from the horse mussel. Leaf disk-puncture assays at 1 mg/mL of stagonolides H-I and modiolide A were phytotoxic to C. arvense. Only stagonolide H inhibited chicory seedling root growth. The most potent toxin, stagonolide H, indicated selectivity when tested on leaves of eight different plants: Canada thistle was most sensitive to the compound.