The goal of the present thesis is to synthesize a novel picture of the population history of the Eastern Mediterranean, through the application of high-throughput methods in ancient DNA. Despite the historical significance of this area for the sociocultural and technological innovations leading to farming and, later, the formation of the earliest state societies, comprehensive archaeogenomic approaches to understanding mobility and social traditions have been limited. Here, I undertook the analyses of a large assemblage of human remains from collections and institutions across Europe and Asia, leading to more than 200 genomes in total – the largest number ever reported for the Aegean, Anatolia and the Northern Levant. By applying state-of-the-art methods in ancient DNA and population genetics, I could reach a number of notable observations regarding the scale and timing of mobility and migration and the admixture among populations, whose interactions were previously inferred only through their material culture. In addition, my research uncovered hitherto unknown aspects of the micro-history, and cultural practices related to family and marriage rules, thereby enriching the way we understand the organization and beliefs of these past societies.