Changes in DNA methylation pattern of β-glucanase 1 and chitinase in flax seedlings treated with non-pathogenic or pathogenic strains of Fusarium oxysporum and after sensitizing effects of the non-pathogenic strain treated with pathogenic Foln3 at 6, 12, 24, 36, and 48 h after inoculation presented as x-fold change in relation to control. The analysis of the third position in the exon, the first in the intron, and the third in the promoter of β-1,3-glucanase 1 and the first, seventh, and eighth positions in the exon of chitinase was performed by the digestion of genomic DNA by the restriction enzymes HpaII and MspI and then the real-time PCR reaction. The data represent the mean from three biological repetitions. Asterisks mark statistically significant differences (p < 0.05) between the treated samples and their own controls.