Invasive species with migratory behavior and complex life cycles represent a challenge for evaluating natal sites among individuals. Private and government-sponsored initiatives resulted in the successful introduction and naturalization of Chinook salmon (Oncorhynchus tshawytscha) throughout northern and southern Patagonia in South America. Migratory populations of Chinook salmon breed in fresh water, but spend most of their life feeding at sea, forming abundant populations in several watersheds draining into the southeast Pacific Ocean. We used single nucleotide polymorphisms combined with genetic structure and mixed-stock analyses to evaluate natal sites of Chinook salmon at sea caught in one estuary and two coastal locations compared to reference populations from breeding sites in fresh water. Firstly, Bayesian individual-assignment analyses revealed no genetic structure among adults caught off the coast of the Tolten River and migrating (maturing) adults caught in Tolten River estuary, suggesting they likely belong to a single population. Secondly, mixed-stock genetic analyses revealed that most Chinook salmon caught in one estuary and two coastal locations likely originated from spawners from the nearest river (86-96%). Contributions from distant watersheds to mixtures at sea decreased with increasing geographic distance. Our combined genetic evidence points strongly tohomingamong non-native Chinook salmon, whereby most adults return to breed to their natal river amid potentially long-distance migrations through the coast. Mixed-stock genetic analyses provide considerable potential to identify the population of origin of Chinook salmon mixtures caught off the coast. They also seem an appropriate proof of concept to assess homing versus dispersal and infer invasion pathways via long-distance migration.