The epigenome, with its variation of DNA methylation profiles across individuals, has long been of interest as a modifier of the genetic code, as “mutations” reflecting past environments, stochastic events, or genetic regulation. To address this question, we investigated the genetic effects on CG methylation over transposable elements as an inherited epigenetics mark. Through GWAS approaches with natural populations of Arabidopsis thaliana, we discovered that CG methylation variation around pericentromeric regions is significantly affected by a genetic variant of Cell Division Cycle Associated 7 (CDCA7), a major chromatin modifier in vertebrates. Notably, a major CDCA7 allele appears aged, suggesting that A. thaliana experienced a reduction in genome-wide CG methylation levels immediately after speciation from its ancestors. In this presentation, we will discuss the features of the genetic basis of CG methylation and its evolution.