We analyzed the levels and patterns of DNA methylation in 25 dwarf rootstocks and 25 semidwarf rootstocks of Prunus mahaleb by methylationsensitive amplification polymorphism marker(MSAP), in order to explore the correlation between dwarf characteristic and genome methylation modification. The results showed that: (1) 15 pairs were selected from 64 pairs of the MSAP primers. Methylation loci of 25 semidwarf rootstocks of P. mahaleb were 4 577, hemimethylation loci were 336, and full methylation loci were 1 274. The total methylation loci of 25 dwarf rootstocks of P. mahaleb were 4 444, hemimethylation loci were 349, and full methylation loci were 1 383. Ttest and oneway ANOVA showed that the level of full methylation and total methylation in semidwarf group were extremely significantly different than that in dwarf group, and the level of hemimethylation was significantly different between the two groups. Meanwhile, the level of methylation in dwarf group was higher than that in semidwarf group.(2) The singleton loci were 23 and polymorphic loci were 136 in semidwarf group. The singleton loci were 17 and polymorphic loci were 142 in dwarf group. So it was concluded that the methylation polymorphism in dwarf group was higher than that in semidwarf group.(3) Further analysis of the types of polymorphism showed that the frequency of A4 type was higher in dwarf group than that in semidwarf group, and the frequency of A2 type was lower in dwarf group than that in semidwarf group, indicating that the locus of hypermethylation in dwarf group was higher than that in semidwarf group. The research indicated the correlation between dwarf characteristic of P. mahaleb and genome methylation modification from the differences in DNA methylation levels and patterns between dwarf group and semidwarf group. The results might provide theoretical support for further breeding of cherry dwarf rootstock.