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 methylationsensitive 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, phosphoribosylamineglycine ligaselike, cold shock domaincontaining protein 3, photosystem II 47 kD protein, E3 ubiquitinprotein ligase RING1, NADHubiquinone 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 NADHubiquinone 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.