Alterations of DNA methylation patterns of two wheat sorts Al’batros odesskii and Donetskaya-48 whose seeds were irradiated with a low dose rate (3 × 10−7 Gy/s) for 4 months have been studied. Six restriction endonucleases were used in the experiments. Primary distinction in DNA methylation patterns of the studied sorts has been demonstrated. Chronic irradiation resulted in an increase of the methylation level on the recognion site for GluI and Sou3AI and in a decrease of this index in recognion sites for endonucleases GlaI and HpaII. The alterations of the methylation level in recognition sites for restrictases MboI and MspI were not found. The considerable increase of chromosome aberration level at the same dose of chronic irradiation has been shown. The role of DNA methylation pattern changes in development of irradiation damage and organism protective reactions is discussed.