Identifying changes in gene regulation that shaped human-specific traits is critical to understanding human evolution. Here, we use >60 DNA methylation maps of different human groups, both present-day and ancient, as well as six chimpanzee maps, to detect regulatory changes that emerged specifically in modern humans. We show that genes affecting vocalization and facial features went through particularly extensive changes in methylation. Especially, we identify expansive changes in a network of genes regulating skeletal development (SOX9, ACAN and COL2A1), and in NFIX, which controls facial projection and voice box (larynx) development. We propose that these changes might have played a key role in shaping the human face, and in forming the human 1:1 vocal tract configuration that is considered optimal for speech. Our results provide insights into the molecular mechanisms that underlie the modern human face and voice, and suggest that they arose after the split from Neanderthals and Denisovans.