Secondary metabolites are a diverse group of molecules that help to compatibility of plants especially in face of stress. Flavonoids and anthocyanins are parts of these compounds. In this study, effect of manganese (concentration of 80 ppm) on enzymatic and non-enzymatic activity rates of cum, 18-21 days after germination, was measured at 4 different times of 0 (control), 24, 48, 72 and 92 hours after stress applying. All of the experiments were performed with 3 independent replications and completely randomized design. Analysis of variance and comparison of means were done using SAS after measurement of different concentrations. Due to manganese stress, content of total flavonoid and anthocyanin and activity of some antioxidant enzymes increased significantly compared to control, as the most enzymatic and non-enzymatic activity rates were observed 48 hours after stress applying. Guaiacol peroxides enzyme showed the most and the least activity rates 24 hours (88.24% higher than control) and 96 hours after stress, respectively. Total results showed that increased flavonoid and anthocyanin after stress applying were consequences of oxidative stress originating from manganese absorption and activation of plant antioxidant system.