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This study explores potential signals of microdifferentiation on the gene pool of three high-altitude populations from Jujuy province (NW Argentina) using highly polymorphic markers. These human communities are characterized by extreme living conditions and very low population densities owing to considerable height above sea level and steep orography. A set of autosomal STRs located at chromosome 6 (6p21.3) was typed in samples from Quebrada Baja (~2,500 m), Quebrada Alta (~ 3,300 m), and Puna (> 3,500 m). Genetic diversity was estimated through the observed (Ho) and expected (He) heterozygosities, and the haplotype diversity. Analyses of the molecular variance (AMOVA) and population differentiation tests based on allele and haplotype frequencies were performed to assess genetic heterogeneity among subgroups. No deviation from HWE expectations was detected for each separate subpopulation; yet, significant departures were detected in the analysis considering the whole area (D6S2792 and D6S105 loci). Overall, genetic diversity showed a decreasing trend as the altitude increases. Thus, allele and haplotype frequencies showed the most significant differences between Puna and Quebrada Baja, which are the populations sited at the edges of the altitude range. The trend to the reduction of the heterozygosity with altitude proves to be compatible with historical patterns of colonization, interregional migration trends, population density, and genetic admixture. The main consequence of the complex mountainous landscape of Jujuy would be an imbalance in the interplay gene flow-genetic drift favoring the latter. The combined effect of restricted gene flow with intense genetic drift would have promoted local genetic differentiation between Jujuy highlands' subpopulations, leading to spatial patterning of the allele frequencies not entirely attributable to geographic distance. Our findings corroborate the effectiveness of STRs to identify microevolutionary changes.