Carmoisine and sunset yellow are organic azo dyes and widely used in food products, drugs and cosmetics. The present study was conducted to evaluate the toxic effects of these colorants on Zea mays with the root and shoot inhibition test, chlorophyll content, a-amylase activity and RAPD PCR technique. In the root inhibition test, EC50 values for carmoisine and sunset yellow were determined as 20 g l(-1) and 22.5 g l(-1), respectively. Chlorophyll a and chlorophyll b levels were decreased when compared to the control group for all of the carmoisine and sunset yellow concentrations. A slight increase was observed in enzyme activity in groups treated with 10 g l(-1) and 20 g l(-1) of carmoisine, while a decrease in enzyme activity was observed in the group treated with 40 g l(-1) of carmoisine. For sunset yellow, a decrease in enzyme activity was observed in all concentrations. In the RAPD test, 71% polymorphism was obtained for carmoisine treated groups. Polymorphism ratio was determined as 53% for the group that was treated with sunset yellow. We concluded that both carmoisine and sunset yellow change the biochemical parameters and have genotoxic effects on Z. mays.