The increasing use of massively parallel sequencing in the study of current and ancient human populations has enabled new approaches to bioanthropological and archaeological issues; however, its application to archaeological samples requires the use of technologies that are not easily accessible outside US and European research centers. To obtain an ancient mitogenome in Argentina, several institutions collaborated to apply massively parallel sequencing and bioinformatic methodologies on an enriched ancient DNA library of an individual from the Beagle Channel (dated 1504 ± 46 years BP), a region of particular interest for this line of inquiry. Phylogenetic reconstruction showed a close relationship with a Yamana from Navarino Island and an individual from Hoste Island (Chilean Antarctic Province): the three shared an ancestor who lived between 203 and 4,439 years ago. These three have mutations reported only for current and ancient individuals from the Beagle Channel, and their relationship with the rest of the D1g sub-haplogroups is unclear. The results obtained here are consistent with the reduction of mobility in the Fuegian archipelago around 4500 years BP that has been proposed based on archaeological evidence.