Abstract:In the present study, the changes of DNA methylation in the barks of epicormic shoots which treated with mechanical wounding in rubber tree were analyzed by methylationsensitive amplification polymorphism (MSAP). The results showed that:(1) in comparison with the control, the levels of DNA methylation were slightly increased at the time point of 0.5 and 2 hours after mechanical wounding. And the larger decrease of DNA methylation levels were observed at 48 hours after mechanical wounding. (2)The main DNA methylation and demethylation events were occurred at 2 and 48 hours, respectively. (3)ATP synthase F1 subunit 1, phosphoribosylamineglycine ligaselike, cold shock domaincontaining protein 3, photosystem II 47 kD protein, E3 ubiquitinprotein ligase RING1, NADHubiquinone oxidoreductase and some hypothetical protein were identified from the differentially methylated sites induced by mechanical wounding. (4)Bisulfite sequencing showed that the both CCGG sites of ATP synthase F1 subunit 1 and NADHubiquinone oxidoreductase were hypomethylated inducing by mechanical wounding. Therefore, the results suggested the DNA methylation may involved in the response of mechanical wounding in epicormic shoots of rubber trees.