The emerging field of Archaeogenetics has been claiming a pivotal role in ongoing efforts to reconstruct the human past. In this thesis, Archaeogenetic approaches are used to reconstruct genomic data from historical and archaeological human remains. These molecular fossils are than used to trace and characterize past human mobility and disease. The papers comprising this thesis are centered around three noteworthy events in human history over the last 15,000 years: the Neolithic transition in central Anatolia; the Bronze Age collapse in the southern Levant; and the Justinianic Plague. The demographic processes that have led to these events are investigated as well as their long term genetic impact.