The archaeogenetics of Europe remains deeply controversial. Advances in ancient DNA analysis have suggested gene flow between Neanderthals and modern humans, who arrived in Europe <50,000 years ago, but have so far failed to support evolution of Neanderthals from a population of Homo heidelbergensis represented by remains in northern Spain. The extent to which European Mesolithic forager populations versus Neolithic pioneers from the Near East contributed to the extant gene pool of Europeans also continues to be contested. Whilst analyses of extant mitochondrial lineages have emphasized Late Palaeolithic and Mesolithic expansions, ancient DNA results suggest significant Neolithic dispersals from the southern “refugial” zone into the northern “bio-tidal” zone. However, whether these had a primarily Near Eastern or north Mediterranean source remains a matter for debate. Meanwhile, ancient DNA has also begun to highlight an important role for later dispersals, especially in the late Neolithic, in shaping the European gene pool.