This is the accepted manuscript. The final version is available from Science at http://www.sciencemag.org/content/345/6200/1255832. ; The New World Arctic, the last region of the Americas to be populated by humans, has a relatively well-researched archaeology but is lacking an understanding of its genetic history. We present genome-wide sequence data from ancient and present-day humans from Greenland, Arctic Canada, Alaska, Aleutian Islands and Siberia. We show that Paleo-Eskimos (ca. 3000 BC-1300 AD) represent a migration pulse into the Americas independent of both Native American and Inuit expansions. Furthermore, the genetic continuity characterizing the Paleo-Eskimo period was interrupted by the arrival of the ancestors of present-day Inuit, with evidence of gene flow between these populations. Despite periodic abandonment of major Arctic regions, a single Paleo-Eskimo meta-population likely survived in near-isolation for more than 4,000 years, only to vanish around 700 years ago. ; We thank the Danish National Sequencing Centre, T. B. Brand and P. S. Olsen for technical assistance, anonymous donors for providing DNA samples, A. Helgason and S. Sunna Ebenesersd?ttir from deCODE for their input on mtDNA phylogenies, A, Di Rienzo for access to genotyping data from Siberian populations, J. R. Southon (BTF), Kitikmeot Heritage Society (TMF), Polar Continental Shelf Project (TMF), Inuit Heritage Trust (DHO?R, JeC, JoC, MGH), Kivalliq Inuit Association (DHO?R, JoC, MGH), communities of Coral Harbor and Chesterfield Inlet (DHO?R, JoC, MGH), Canadian Museum of History (DHO?R, JeC, JoC, MGH), D. Morrison (DHO?R, JeC, JoC, MGH), L. Wood (DHO?R, JoC, MGH), J. Young (DHO?R, JeC, JoC, MGH), D. Stenton (DHO?R, JeC, JoC, MGH), S. Girling-Christie (JeC), Commission for Scientific Research in Greenland (JA), Greenland National Museum & Archives (JA), Parks Canada (MAPR, VG), Memorial University (VG, MAPR), Government of Newfoundland and Labrador (VG), The Rooms Inc. (VG), Innu Nation (VG), Nunatsiavut Government (VG), Miawpukek First Nation (VG), D. Lavers (VG), R. Anstey (VG), W. Jones and Qanirtuuq Inc., Quinhagak, Alaska (KB and RK), the residents of Quinhagak, Alaska (KB and RK), NIMA Corporation, Mekoryuk, Alaska (KB and RK), and the Carnegie Trust for the Universities of Scotland (KB and RK). Supported by the Danish National Research Foundation (EW) Lundbeck Foundation (EW, NL), Villum Foundation (AA), SNSF Fellowship (AS-M, PBSKP3_143259), The Rock Foundation (BG, MA), Social Sciences and Humanities Research Council of Canada (TMF), National Science Foundation Office of Polar Programs (DHO?R: OPP-9974623 and OPP-0327641; JoC: OPP-9726126 and OPP-9977931; MGH: OPP-9813044), Northern Worlds Initiative (HCG), Augustinus Foundation (HCG), the Danish Council for Independent Research (IM), National Science Foundation (JA: IPY grant 0732327; MHC, OPP-9905090 and OPP-0327676), Wenner-Gren Foundation for Anthropological Research (MGH: No. 6364), Natural Sciences and Engineering Research Council of Canada Postgraduate Fellowship (MGH), University of Utah Graduate Research Fellowship (MGH), EU Marie Curie FP7 Initial Training Network Grant (MaR: FP7-ITN-215362-2), Arts and Humanities Research Council (KB and RK: AH/K006029/1), Memorial University Faculty of Arts Research Initiative (VG), Memorial University Office of Research Grant (VG), Social Sciences and Humanities Research Council of Canada (MAPR), EU European Regional Development Fund through the Centre of Excellence in Genomics to Estonian Biocentre (MM and RV), Estonian Institutional Research (MM and RV: grant IUT24-1), and, Estonian Science Foundation (MM and RV: grant 8973. Informed consent was obtained for the genome sequencing of the modern individuals, with ethical approval from The National Committee on Health Research Ethics, Denmark (H-3-2012-FSP21). Sequence data for the ancient samples are available for download through European Nucleotide Archive (ENA) accession number XYZ, while those for the modern populations are available for demographic research under data access agreement with EW. The authors declare no competing financial interests.