DNA methylation is a central epigenetic modification that is established by de novo DNA methyltransferases like Dnmt3a. The mechanisms underlying the generation of genomic methylation patterns are still poorly understood. In a collaboration with the group of Prof. F. Fuks from the Laboratory of Cancer Epigenetics of the Universite´ Libre de Bruxelles, we demonstrate here that CK2 phosphorylates endogenous Dnmt3a at two key residues, thereby downregulating the activity of Dnmt3a. Genome-wide DNA methylation analysis shows that CK2 primarily modulates CpG methylation of several repeats, most notably of Alu SINEs, which lost methlyation. We also show that CK2-mediated phosphorylation is required for localization of Dnmt3a to heterochromatin. By revealing phosphorylation as a mode of regulation of de novo DNA methyltransferase function our results shed light on the origin of DNA methylation patterns.