Allelopathy can affect the growth of cereals and crops in their natural habitats. The current investigation was conducted to evaluate the allelopathic effects of A. arvensis and A. cotula aqueous leaf extracts on Vicia faba. The mutagenic and genotoxic effects of each extract were assessed on mitotic and meiotic cells of faba through a cytogenetic method and polymorphisms in the banding profiles of seed proteins using SDS-PAGE. Faba seeds were separately treated with three different concentrations of aqueous extracts (5, 10 and 20%) for 6 and 12 h. According to cytogenetic data, faba exhibits a significant frequency of chromosomal abnormalities as well as obstruction of mitotic and meiotic activities which are concentration and period exposure dependent. At 20% concentration of A. arvensis, the maximum values of the mitotic index (16.73 for 6 h and 16.51 for 12 h) were compared to the control 13.58 and 12.98 respectively. A. cotula caused a strong inhibition in the mitotic activity and reached its minimum values (2.17 for 6 h and 0.83 for 12 h) compared to the control (13.58 and 12.98 respectively). Aqueous extracts of A. cotula are more effective than those of A. arvensis for inducing the genotoxic action in PMCs of the 1st and 2nd meiotic divisions. The changes in protein were illustrated by the appearance and disappearance of some bands, changes in band intensity and the relative mobility of some bands. The results confirmed that the allelochemicals in A. arvensis and A. cotula extracts caused potential cytotoxic and genotoxic effects and a change in the protein pattern of faba.