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Recent studies have expanded and refined the founding haplogroups of the Americas using whole mitochondrial (mtDNA) genome analysis. In addition to pan-American lineages, a number of studies have identified specific variants that show higher frequencies in restricted geographical areas. In order to further characterize Native American maternal lineages and specifically examine local patterns within South America, we analyzed twelve maternally unrelated Yekuana whole mtDNA genomes from one village (Sharamaña) that include the four major Native American haplogroups A2, B2, C1, and D1. Our study proposes a reconfiguration of one subhaplogroup A2 (A2aa) that is specific to South America and identifies other singleton branches across the four haplogroups. Furthermore, we show nucleotide diversity values that increase from north to south for haplogroups C1 and D1. The results from our work add to the growing mitogenomic data that highlight local phylogenies and support the rapid genetic differentiation of South American populations, which has been correlated with the linguistic diversity in the region by previous studies.