The effects of fluoride (Fl) emission, from an aluminum (Al) reduction plant in Iran, on the concentration of Fl in six legume species were studied. In addition, the influence of Fl on leaf flavonoids was investigated. Determination of Fl in collected plants (Alhagi camelorum Fisch., Cercis siliquastrum L., Glycyrrhiza glabra L. Medicago sativa L., Robinia peseudoacacia L., and Sophora alopecuroides L.) from the factory area was performed using a Fl ion-selective electrode. Identification of flavonoids in the samples was obtained by two-dimensional paper chromatography (2-D PC) and thin layer chromatography (TLC). Controls were obtained from plants located 10 km distance from the factory. Results showed high Fl concentration in all polluted samples. Phytochemical changes in polluted leaves were observed with appearance or disappearance of some flavonoids.