Objectives: This study aims to characterize the genetic histories of ancient hunter-gatherer groups in Fuego-Patagonia (Chile) with distinct Marine, Terrestrial, and Mixed Economy subsistence strategies. Mitochondrial (mtDNA) and Y-chromosome data were generated to test three hypotheses. H 0 : All individuals were drawn from the same panmictic population; H 1 : Terrestrial groups first populated the region and gave rise to highly specialized Marine groups by $7,500 cal BP; or H 2 : Marine and Terrestrial groups represent distinct ancestral lineages who migrated independently into the region. Methods: Ancient DNA was extracted from the teeth of 50 Fuegian-Patagonian individuals dating from 6,895 cal BP to after European arrival, and analyzed alongside other individuals from previous studies. Individuals were assigned to Marine, Terrestrial, and Mixed Economy groups based on archeological context and stable isotope diet inferences, and mtDNA (HVR1/2) and Y-chromosome variation was analyzed.