The transition to a farming lifestyle was one of the major episodes of innovation in the history of our species and it has been the subject of intense archaeological research for decades1. In the past few years, archaeogenetic studies have been crucial in resolving some of the longstanding questions about the Neolithisation of Europe2-6. Here, we analyse new genome sequence data from 13 early farmers from Spain and compare them to previously published modern day and ancient genomes from Europe, North Africa and the Near East. We show that the first farmers to arrive to the Iberian Peninsula during the Neolithic, followed a coastal Mediterranean route bringing farming practices with them. These Neolithic individuals show a similar genetic structure across the North, North East and South of Iberia with no evidence of north African influence. Furthermore, we observe a certain degree of genetic differentiation between Early Neolithic Iberian and Central European farmers. An indication of at least two founding populations of early Neolithic Europeans (one that arrived via the Mediterranean coast and the other via the Danube basin into Central Europe). Among all early European farmers the Iberian Neolithic groups show the highest genetic affinities to present-day Sardinians suggesting that the modern population of the island are relatively direct descendants of these early Mediterranean farmers. Later, Iberian Chalcolithic populations derive from the interbreeding between incoming farmers and native hunter-gatherers3. In turn, these Chaloclithic groups are closely related to modern day Basques whom appeared to be isolated since the Late Neolithic3. Finally, genetic similarities between Middle to Late Neolithic farmers from Ireland and Iberia potentially suggest the latter to be the origin of the Megalithic culture which spread along the Atlantic coast and later reached the British Isles and Scandinavia7.