Medicinal plants are an inexhaustible source of secondary metabolites, namely polyphenols including flavonoids, alkaloids and terpenoids, which generate various biological activities. Keeping this in mind, we were interested in a spontaneous plant Peganum harmala L. to demonstrate the antimitotic and genotoxic effect of the alkaloid and flavonoid fractions (aqueous and butanolic) of the leaves of this species on root meristematic cells of Allium cepa L. Mitotic indices, phase indices, aberration indices as well as cytotoxicity limit values were calculated for our different samples and controls, namely the negative (distilled water) and positive controls (colchicine 1mg/ml and quercetin 1mg/ml). The results indicate a mitodepressant and sublethal effect, observed with the alkaloid and flavonoid fractions of the leaves of Peganum harmala L. Exposure of meristematic cells to the samples resulted in an antimitotic and genotoxic effect translated into a large number of chromosomal, nuclear and cellular aberrations.