A structure-activity relationships study was conducted assaying 15 natural analogues and derivatives belonging to two groups of organic compounds, nonenolides and cytochalasins, for their toxicity against the composite perennial weeds Cirsium arvense and Sonchus arvensis occurring through the temperate region of world. The toxic nonenolides (stagonolide, putaminoxin, pinolidoxin) and cytochalasins (deoxaphomin, cytochalasins A, B, F, T, Z2 and Z3) were isolated from phytopathogenic Stagonospora, Phoma and Ascochyta spp. The pinolidoxin (7,8-O,O'-diacetyl- and 7,8-O,O'-isopropylidene-pinolidoxin) and cytochalasins B (21,22-dihydro-, 7-O-acetyl- and 7,20-O,O'-diacetyl-cytochalasin B) derivatives were obtained by chemical modifications of the corresponding toxins. Among the 15 compounds tested, stagonolide and deoxaphomin proved to be the most phytotoxic to C. arvense and S. arvensis leaves, respectively. The tested phytotoxic nonenolides were stronger inhibitors of photosynthesis in C. arvense leaves than cytochalasines A and B. Stagonolide had less effect on membrane permeability in C. arvense leaves than cytochalasin B. Significant changes of light absorption by C. arvense leaves in visible and infrared spectra were caused by stagonolide. The functional groups and the conformational freedom of the ring, appear to be important structural features for the nonenolides toxicity, whereas and the presence of the hydroxy group at C-7, the functional group at C-20 and the conformational freedom of the macrocyclic ring are important for the cytochalasins toxicity.