Genomic DNA, which contains all of the genetic information, is damaged by a variety of endogenous and environmental factors such as genotoxic chemicals, ionizing radiation and UV light. Consequently, the DNA repair process is constantly active as it responds to damage in the DNA structure. Not only cardiotoxicity of anticancer drug treatment but also ischemic heart disease and heart failure associated with overloaded pressure interfere with DNA damage response and DNA repair regulation in cardiomyocytes. DNA methylation, catalyzed by the DNMTs, plays an important role in maintaining genome stability, but the molecular mechanism is not clear. In this study, we examine and outline the links between DNA methylation and the DNA damage repair systems and discuss the possible mechanisms of how they are orchestrated, with a focus on cardiotoxicity of anticancer drugs.