DNA methylation is a general epigenetic mechanism for plants, animals, and fungi to adapt to environmental variation. Two biotypes of the Russian wheat aphid (Diuraphis noxia), Biotype 1 and Biotype 2, have different virulence to host plants. In this study, in addition to a high polymorphism, DNA methylation at cytosines were observed in genomic fragments of four genes in Biotype 1 and Biotype 2, after the genomic DNA was treated with sodium bisulfite. These genes presumably encode proteins and enzymes in salivary glands of aphids. The two Biotype 1 showed different methylation levels, that is, Biotype 1 showed a higher methylation on the four genes. Two thirds of methyl cytosines were in a sequence context of CHH (H = A, C, or T). Some polymorphism and methylation sites were located at important positions in terms of enzyme function, such as close to catalytic residues or inhibitor binding residues. These findings may provide clues to explore the evolutionary mode between Russian wheat aphid virulence and resistance genes of host plants.