There are many unanswered questions about the population history of the Central and South Central Andes, particularly regarding the impact of large-scale societies, such as the Moche, Wari, Tiwanaku, and Inca. We assembled genome-wide data on 89 individuals dating from ∼9,000-500 years ago (BP), with a particular focus on the period of the rise and fall of state societies. Today's genetic structure began to develop by 5,800 BP, followed by bi-directional gene flow between the North and South Highlands, and between the Highlands and Coast. We detect minimal admixture among neighboring groups between ∼2,000–500 BP, although we do detect cosmopolitanism (people of diverse ancestries living side-by-side) in the heartlands of the Tiwanaku and Inca polities. We also highlight cases of long-range mobility connecting the Andes to Argentina and the Northwest Andes to the Amazon Basin.Video AbstracteyJraWQiOiI4ZjUxYWNhY2IzYjhiNjNlNzFlYmIzYWFmYTU5NmZmYyIsImFsZyI6IlJTMjU2In0.eyJzdWIiOiI5ZTJmZjA2Y2Y3NzBkOTE2YWRiOWJmZGYyODdkN2FlZCIsImtpZCI6IjhmNTFhY2FjYjNiOGI2M2U3MWViYjNhYWZhNTk2ZmZjIiwiZXhwIjoxNjMyMDEyNjg4fQ.q1opfhSnVRpLzJJPWJTcccPEjUFmtiYXJZJagxcOocE7keapAbeZUmo1Haw5cv1y1TdWKT6KkrDNoC5Js1tTLj6kcV_FFA6xdzX7GCelcdmXM13xl-v1K8pdiU7bHSpfYUvb93BRiCBD9aj0pz-U0yCG4C51MgvypoqVP7kY5X7rC-0YQGRQNxmaoXPsXjOma7_NPOPDCUc0OP21aKYk_LO8eF-4lOb_3g6aNyPXM5txsfBhZP0s1PUwgfD2Ky460_nSKcBhpwjFQjwirFfQFpQ2Yphgkvm9PLqo-g-wVcWNXHrEPz0iDEHs_XDHlVnXBGm5_RUhYahM4lGOZW4yjg(mp4, (26.07 MB) Download video