Although previous studies have characterized genetic structure throughout much of the range of Merganetta armata (Torrent Duck), Patagonian populations have not been included. This study presents the first genetic analysis of the Patagonian population and situates it within the broader evolutionary context of the species. Here, we identify a divergent Patagonian mitochondrial DNA (mtDNA) lineage distinct from all other known subspecies. Our analyses further reveal that the traditionally recognized berlepschi and garleppi forms are nearly indistinguishable and cluster closely with armata, thereby challenging established taxonomic boundaries. These findings suggest that Patagonian M. armata may constitute an Evolutionarily Significant Unit of conservation concern. Feathers from 41 individuals were sampled across the Southern Andes, including the Yungas, High-Andes headwaters, and Patagonian Forests regions (22-50 degrees S). During this study, we sequenced the mitochondrial control region and estimated population genetic and demographic parameters. In particular, we evaluated structure and connectivity through haplotype networks, principal component analysis, phylogenetic inference, and Bayesian divergence dating. This approach revealed fine-scale structuring and restricted gene flow, as well as unexpected affinities among northern and central lineages. The analyses also underscored the deep isolation and evolutionary distinctiveness of the Patagonian clade. Our mtDNA dataset, augmented with previously published sequences, provides broad geographic coverage across the species' distribution. The results are consistent with hybridization, paraphyly, and riverine connectivity shaping subspecific limits in Merganetta. Pleistocene glacial cycles likely reinforced the isolation of the Patagonian lineage. Together, these insights underscore the importance of integrating phylogeography and ecology to redefine M. armata subspecies and conserve the unique diversity of Andean waterfowl. We analyzed 41 Merganetta armata (Torrent Duck) from 6 locations across the southern Andes, finding low local genetic diversity but strong differentiation among locations, structured by river systems and geographic isolation. We identified a distinct Patagonian evolutionary unit, likely shaped by past glaciations and currently isolated by arid regions, underscoring the need for targeted conservation amid threats such as invasive species, pollution, and tourism. Our results are consistent with the presence of hybrid zones where subspecies ranges meet (Yungas and High Andes), underscoring the importance of maintaining natural corridors and managing hybridization processes. Morphological subspecies did not consistently match genetic lineages, revealing a more complex taxonomic structure than previously recognized. The current patterns of genetic variation likely reflect the combined effects of past climate change, hybridization, river connectivity, and historical isolation. In summary, this study improves understanding of the evolutionary history of this charismatic duck species and provides key insights into its taxonomy and conservation. Previamente, se ha caracterizado la estructura gen & eacute;tica en buena parte del rango de distribuci & oacute;n de Merganetta armata (Pato de los Torrentes), llamativamente, sin haberse incluido las poblaciones patag & oacute;nicas. Aqu & iacute;, se presenta el primer an & aacute;lisis gen & eacute;tico de la poblaci & oacute;n patag & oacute;nica, situ & aacute;ndola en un contexto evolutivo amplio de la especie. Identificamos un linaje de ADN mitocondrial (mtDNA) patag & oacute;nico divergente, distinto de todas las dem & aacute;s subespecies conocida, que podr & iacute;a ser una Unidad Evolutivamente Significativa de inter & eacute;s para la conservaci & oacute;n. Adem & aacute;s, nuestros an & aacute;lisis revelan que las variantes morfol & oacute;gicas conocidas como berlepschi y garleppi tienen linajes pr & aacute;cticamente indistinguibles y se relacionan estrechamente con armata, lo que cuestiona los l & iacute;mites taxon & oacute;micos establecidos. Se muestrearon plumas de 41 individuos a lo largo de la Cordillera de los Andes, incluyendo las Yungas, las cabeceras altoandinas de Cuyo y los bosques patag & oacute;nicos (22-50 degrees S). Se extrajo ADN de las muestras, del cual se secuenci & oacute; la regi & oacute;n de control mitocondrial. Se estimaron par & aacute;metros gen & eacute;ticos poblacionales y demogr & aacute;ficos, y se determin & oacute; la estructura y la conectividad mediante redes de haplotipos, an & aacute;lisis de componentes principales, inferencia filogen & eacute;tica y dataci & oacute;n de divergencia bayesiana. Estos an & aacute;lisis revelaron una estructuraci & oacute;n geogr & aacute;fica y un flujo g & eacute;nico acotado, as & iacute; como conexiones inesperadas entre linajes de las Yungas y Cuyo. Los an & aacute;lisis tambi & eacute;n destacaron el profundo aislamiento y la diferenciaci & oacute;n evolutiva del clado patag & oacute;nico, posiblemente debido a los ciclos glaciales pleistoc & eacute;nicos. Nuestro conjunto de datos de mtDNA, complementado con secuencias previamente publicadas, proporciona una amplia cobertura a lo largo de la distribuci & oacute;n de la especie. Los resultados son consistentes con la hibridaci & oacute;n, la parafilia y la conectividad fluvial como factores que moldean los l & iacute;mites subespec & iacute;ficos en Merganetta. En conjunto, estos resultados subrayan la importancia de integrar la filogeograf & iacute;a y la ecolog & iacute;a para redefinir las subespecies de M. armata y conservar la diversidad & uacute;nica de las aves acu & aacute;ticas andinas.