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We report the incidence and distribution of Native American mtDNA haplogroups in nine villages across the Sierras Centrales archeological area, located in central Argentina. The aims of the study were (1) to investigate the relative incidence of native maternal lineages, (2) to determine whether or not the homogeneous pattern observed in a previous study persists at this larger scale, and (3) to ascertain the genetic affinities between the studied population and other native populations of the Southern Cone of South America. Of the 310 individuals from whom DNA was extracted, 249 (80.3%) were assigned to one of the founding native American haplogroups. This finding confirms the persistence at high prevalence of native maternal lineages in the rural populations of central Argentina. The haplogroup distribution is homogeneous in the population samples from Córdoba province, with haplogroups C and D always found at the highest frequencies. The sample from San Luis province, Tilisarao, presents a different genetic pattern, with haplogroups A and B being the most frequent. Principal components analysis and SAMOVA at the regional level show that the Córdoba, Patagonia, and Tierra del Fuego populations cluster together, which suggests a common origin.