Salmonid introductions for sport fishing and, more recently, for farming, have had a large impact on freshwater ecosystems in many regions worldwide. In Patagonia, both activities have contributed to the colonization of freshwater systems particularly by species such as Brown Trout (Salmo trutta) and Rainbow Trout (Oncorhynchus mykiss). The ecological impact of these species has been widely studied in continental freshwater ecosystems. There are, however, no studies of their impact in southern Patagonian fjords. Here, we evaluate the effect of the presence of Coho Salmon (Oncorhynchus kisutch) and Chinook Salmon (Oncorhynchus tshawytscha) juveniles on the diet (stomach content and isotopic niche) of the native Galaxias maculatus in lakes and estuaries associated with Patagonian fjord system. Galaxias maculatus inhabiting salmon-free lakes fed primarily on insects, while lake G. maculatus coexisting in sympatry with Coho Salmon consumed primarily benthic macroinvertebrates. In estuaries, the diet of G. maculatus and Salmon (Coho and Chinook) overlap. The isotopic niche space of G. maculatus (based on carbon, nitrogen and sulphur isotopic compositions) was larger in lake where it was found in sympatry with Coho Salmon compared to its isotopic niche space in salmonid-free lakes. Finally, in estuaries, niche spaces were similar between G. maculatus and Coho Salmon. The niche space was greater for Chinook Salmon than for G. maculatus and Coho Salmon, most probably as a consequence of their territorial behaviour and larger home ranges.