Significance Beringia gave rise to the first Western Hemisphere colonists, although the genetic characterization of that source population has remained obscure. We report two mitogenomes from human remains within Beringia, with an age (∼11,500 cal B.P.) that postdates the end of the initial colonization by only a few millennia. The mitochondrial lineages identified (B2, C1b) are rare to absent in modern northern populations, indicating greater genetic diversity in early Beringia than in modern populations of the region. The antiquity and geographic location of these two burials, and the combined genomic and archaeological analyses, provide new perspectives on the link between Asia and the Americas, and the genetic makeup of the first Americans.