||Genetic information from human remains obtained from archaeological excavations can reveal the history of modern peoples, rediscover the signature of prehistoric populations, and track human variation across time and space. The events that led to the colonization of the Americas can be explored by sequencing geographically and temporally appropriate samples. Two distinct phases of Native American migrations are investigated here â€" the initial Pleistocene movement of people out of Beringia and into North America, and the much later Holocene migrations eastward across the North American Arctic. In the first chapter, whole mitochondrial genomes were sequenced from two contemporaneous human burials at a rare Pleistocene residential site at Upward Sun River in central Alaska, dating to âˆ¼11,500 cal B.P. One individual carried mitochondrial lineage C1b, whereas the other carried a root B2 haplotype. Today C1b and B2 are absent in modern populations of northern North America. These results validate the previously hypothesized expectation of higher levels of genetic diversity in the earlier, and now lost, Beringian gene pool. The second and third chapters concern the origins and migrations of the Neo-Eskimo Thule, the hypothesized ancestors of modern day IÃ±upiat/Inuit. A population-scale sequencing project was initiated from a cemetery at Nuvuk, a long-term Thule village at Pt. Barrow, AK. The cemetery represents the oldest and largest number of Thule remains ever found in North America. The hypervariable segment I of the mitochondrial genome was amplified and sequenced in 44 individuals, and Arctic haplogroups A2a, A2b, and D4b1a2a1a were identified. The haplogroup frequencies at Nuvuk were compared to populations across Siberia and North America, and were most similar to the modern Inuit communities of Canada and Greenland. This supports the ancient North Slope as the origin point for the Thule migrations. To further investigate phylogenetic relationships, additional human remains were sampled from Igliqtiqsiugvigruaq, a 19th century interior Alaskan site located inside the boundary of Kobuk Valley National Park. Whole mitochondrial genomes were sequenced from three Nuvuk burials and three remains from Igliqtiqsiugvigruaq, and these allowed a refinement of the haplogroup A2b and D4b1a2a1a phylogenies.