In the mammalian genome, numerous CpG‐rich loci define tissue‐dependent and differentially methylated regions (T‐DMRs). Euchromatin from different cell types differs in terms of its tissue‐specific DNA methylation profile as defined by these T‐DMRs. G9a is a euchromatin‐localized histone methyltransferase (HMT) and catalyzes methylation of histone H3 at lysines 9 and 27 (H3‐K9 and ‐K27). To test whether HMT activity influences euchromatic cytosine methylation, we analyzed the DNA methylation status of approximately 2000 CpG‐rich loci, which are predicted in silico, in G9a^−/− embryonic stem cells by restriction landmark genomic scanning (RLGS). While the RLGS profile of wild‐type cells contained about 1300 spots, 32 new spots indicating DNA demethylation were seen in the profile of G9a^−/− cells. Virtual‐image RLGS (Vi‐RLGS) allowed us to identify the genomic source of ten of these spots. These were confirmed to be cytosine demethylated, not just at the Not I site detected by the RLGS but extending over several kilobase pairs in cis. Chromatin immunoprecipitation (ChIP) confirmed these loci to be targets of G9a, with decreased H3‐K9 and/or ‐K27 dimethylation in the G9a^−/− cells. These data indicate that G9a site‐selectively contributes to DNA methylation.