Methylation of DNA, the fundamental epigenetic layer of the genome, regulates gene expression. In previous work, we developed methods to reconstruct DNA methylation patterns in ancient DNA (Gokhman et al., Science, 2014). Since the DNA sequence of our closest archaic ancestors, the Neanderthals and the Denisovans, is so similar to ours, there a limit on what we can learn by simply comparing DNA sequences. Using our methods, we identified regions that are differentially methylated between archaic and modern humans, and were able to assign genes to many, but not all, of these regions. In the current work, we wished to expand the list of “differentially methylated genes” by using the three-dimensional information of our genome. We therefore generated a consensus 3D organisation map of the human genome and linked dozens of regions which are differentially methylated between modern and archaic humans, to their target genes. Remarkably, we found that these genes are involved in vocal and facial anatomy, reinforcing our recent findings (Gokhman et al., Nat Commun, 2020) as well as spinal cord, chin, hair and scalp. This supports the hypothesis that many of the differences between modern and archaic human are epigenetic in nature.