All cells in a mammalian body share the same DNA content but have a distinct appearance and function. This is achieved by activation and repression of genes by epigenetic mechanisms, which are crucial for stable differentiation of cells in a multi-cellular organism. DNA methylation, established by DNA methyltransferase (DNMT) enzymes, regulates gene expression and is essential for mammalian development. Histone tail post-translational modifications modulate the recruitment and activity of DNMTs. In particular, the PWWP domains of DNMT3A and DNMT3B are posited to interact with histone 3 lysine 36 trimethylation (H3K36me3). In this study, I characterise a mouse model carrying a D329A point mutation in the DNMT3A PWWP domain, predicted to ablate the DNMT3A-PWWP and H3K36me3 interaction. Similar mutations in humans cause primordial dwarfism. I found that oocytes of Dnmt3a-D329A mice show no alterations in DNA methylation. However, the D329A mutation causes dominant postnatal growth retardation in mice. At the molecular level, it results in aberrant progressive acquisition of DNA methylation across domains marked by H3K27me3 and bivalent chromatin in multiple adult tissues. These domains characteristically contain important developmental regulatory genes, and their aberrant methylation is associated with de-repression of these genes in the adult hypothalamus. Recapitulation of this mutation in mouse embryonic stem cells (mESCs) did not identify new DNMT3A-D329A interacting partners. Upon differentiation of Dnmt3a-D329A carrying mESCs to neuronal progenitor cells, a minor gain in DNA methylation is observed. This work provides key molecular insights into the role of DNMT3A in regulating postnatal growth, the targeting of DNMT3A to the genome, function of the DNMT3A PWWP domain and its association with histone modifications.