Phytotoxic effect of biochanin A (a major isoflavone in clover) on different weed species was evaluated in agar medium bioassays. Silene noctiflora and Geranium molle roots growth were progressively inhibited with increasing concentrations of biochanin A, whereas the monocot species (Echinochloa crus-galli) were unaffected. With regard to the dicot species, S. noctif lora (EC50 = 35.80 ?M and EC25 = 5.20 ?M) was more susceptible than G. molle (EC50, EC25 > 400 ?M). S. noctif lora, G. molle, and E. crus-galli root and shoot samples, representing a susceptible, a less susceptible, and a nonsusceptible species, respectively, were analyzed by LC-MS to quantify biochanin A and its transformation products. Biochanin A and its known transformation products genistein, dihydrobiochanin A, pratensein, and p-coumaric acid were quantified. Sissotrin was identified and quantified while assigning unknown peaks. The treated root samples contained more biochanin A, genistein, pratensein, and dihydrobiochanin A than shoot samples.