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 H-1, C-13, 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 Q(A), 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.