Four compounds, the flavone linarin (1), the triterpene lupenone (2), the tocopherol (vitamin E, 3), and the new natural alkaloid 1,2,3,4-tetrahydro-1,1-dimethyl-6,7-isoquinolindiol (affineine, 4), were the major natural products isolated from Zanthoxylum affine (syn. Zanthoxylum fagara, Rutaceae). Compound 1 is highly abundant in this plant and was isolated as a white precipitate obtained from the acetone and methanol extracts. The structure of these four compounds was established by 1D and 2D NMR spectroscopy including 1H, 13C, DEPT, COSY, HSQC, and HMBC experiments. The hexane, acetone, and methanol extracts, as well as 1, were evaluated for their potential phytotoxic effects in pre- and post-emergent assays, as well as to identify their mechanisms of action. As pre-emergent phytotoxic agents, the hexane, acetone, and methanol extracts inhibited germination and residual growth (root and stem elongation) of Lactuca sativa (lettuce) and Lolium perenne (perennial ryegrass). As post-emergent agents, they inhibited dry biomass. Compound 1 acts as a pre-emergent herbicide, by inhibiting germination, seed respiration, residual seedling growth and, notably, root hair development. Furthermore, 1 inhibited the synthesis of ATP and the electron transport chain of isolated spinach chloroplasts; in this way, it behaves as a Hill reaction inhibitor. The site of inhibition was located at the donor site of PSII from the oxygen evolving complex to QA, thus acting as a multisite compound. These results suggest that compound 1 can be used as a lead for a potential green herbicide with different targets.