DNA methylation is a prevalent epigenetic modification involved in transcriptional regulation and essential for mammalian development. While the genome‐wide distribution of this mark has been studied to great detail, the mechanisms responsible for its correct deposition, as well as the cause for its aberrant localization in cancers, have not been fully elucidated. Here, we have compared the activity of individual DNMT3A isoforms in mouse embryonic stem and neuronal progenitor cells and report that these isoforms differ in their genomic binding and DNA methylation activity at regulatory sites. We identify that the longer isoform DNMT3A1 preferentially localizes to the methylated shores of bivalent CpG island promoters in a tissue‐specific manner. The isoform‐specific targeting of DNMT3A1 coincides with elevated hydroxymethylcytosine (5‐hmC) deposition, suggesting an involvement of this isoform in mediating turnover of DNA methylation at these sites. Through genetic deletion and rescue experiments, we demonstrate that this isoform‐specific recruitment plays a role in de novo DNA methylation at CpG island shores, with potential implications on H3K27me3‐mediated regulation of developmental genes.