American mink Mustela vison, originally bred in fur farms, have become established in areas occupied by native endangered Southern river otter Lontra provocax, in Patagonia. In accordance with European experience, this biological invasion in South America raises questions about the interaction between invasive mink and native otter, from the viewpoints of both community assembly and conservation. We set out (1) to find which aspects of habitat structure were related to the distribution of signs of both this invasive species and Southern river otter Lontra provocax, in Argentinean Patagonia and their most common prey and (2) to test general predictions of niche partitioning between these two species. Based on surveys of 447 of 600 m transects for otter and mink scats/footprints along the waterside of lakes and rivers in the Andean Patagonian region, we compared diet composition (from scat analysis) and micro-habitat preferences (from field signs) of the two species. Otters were more specialist than mink in habitat use and diet. Mink used different habitats in other river basins where otters were absent. Where they occurred together in the basin of the Limay River, the distributions of their signs were similar, and mink diet was more similar to that of otters. There was no detectable difference in otter diet before and after mink arrival in the Limay basin. Contrary to the prediction of niche partitioning, and to the findings of European studies, resource use by mink was more similar to that of otters where the species occurred sympatrically than where they were allopatric.