In recent years cultivated soils have been increasingly supplemented with nutrients that at low doses are necessary for proper plant functioning but become toxic at high doses. New methods are needed to prevent these destructive actions, and for this reason we studied the effects of two elements – Mn treated as a stressor and Se treated as a potential defense in two wheat cultivars. The intensity of stress was manifested in tissue browning and weight reduction and was determined by an increase in lipid peroxidation and quantitative analysis of hydrogen peroxide levels. It was found that the excess of Mn in the substrate caused more intense changes in these indicators in the root system than in the leaves, and that Se presence partly eliminated the stress evoked effects. Moreover, Mn-treatment was accompanied by a greater absorption of this element by the roots, and a reduced uptake of other elements (K, Fe, S, P), with the exception of Ca, an increase in which was observed especially in the additional presence of Se. It was suggested that the rise in Ca level can lead to modification of cell differentiations and may be one of the steps in defense mechanisms. The change in the direction of cell differentiation in the apical part of the root was observed microscopically under Mn stress and was accompanied by a quantitative increase in 5-met C. Based on DNA methylation profiles detected by MSAP we concluded that various types of methylation sites may be activated under Mn treatment in roots.