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The genetic composition of Amerindian descendants from Patagonia has long been a focus of interest, although the information available is still scarce for many geographic areas. Here, we report the first analysis of the variation in the mtDNA control region for an area of northwestern Patagonia, the North of Neuquén, with the aim of studying the processes and historical events that modeled the evolutionary history of these human groups. We analyzed 113 individuals from two localities of northern Neuquén, along with 6 from southern Neuquén and 223 mtDNA sequences previously published from neighboring areas from Argentina and Chile. We estimated the haplotypic variation and spatial structure of molecular variability. Amerindian subhaplogroups predominate in the two samples from northern Neuquén (N= 70), being D1g and C1b13 the most represented, although in different proportion. These samples exhibit Amerindian mtDNA haplotypes similar to the variants from neighboring areas. Most of haplotype variability is observed within group, while variation among groups is relatively low and scarcely associated to geographical space. The most frequent subhaplogroups in northern Neuquén are characteristic of native populations from Patagonia and Chilean Araucania, and probably originated in the region during the Late Pleistocene or Early Holocene. However, the spatial variation of mtDNA haplotypes departs from a latitudinal pattern and suggests differential levels of gene flow among areas during the Late Holocene; with moderate levels across the North of Neuquén as well as between this area and neighbouring populations from Chile and the South of Neuquén and Río Negro.