Salmonids have been introduced into the rivers and lakes of southern South America since the 1900's, principally for recreational fishing purposes (Golusda 1907, Basulto 2003, Pascual & Ciancio 2007). Introduction of Chinook salmon (Oncorhynchus tschawytscha Walbaum) to southern Chile (between 38.7°S and 54.7°S) occurred in five stocking events during the 1970's with the planting of both eggs and alevins from Washington State, U.S.A. (Joyner 1980, Dufflocq 1981, Donaldson & Joyner 1983, Basulto 2003, Pascual & Ciancio 2007), but these initial introductions were described as failures (Basulto 2003). More recently, since the 1980's, there has been a development in intense salmon farming between 40.7°S and 53°S, with Chinook salmon constituting less than 5% of total Chilean farmed fish production (SERNAPESCA 2006). At present, mature salmon have been detected, in Chile, returning to the rivers Pratt (Basulto 2003), Futaleufu (Di Prinzio 2001), and Petrohué (Soto et al. 2006, 2007), and in the Argentinean Patagonia (Di Prinzio 2001, Pascual & Ciancio 2007, Becker et al. 2007). The Petrohué River is of great relevance because it is the only site with documented Chinook salmon spawning sites and juveniles (Soto et al. 2006, 2007). However, it is not clear whether these returning individuals have escaped from farming net pens or are descendents of the first individuals introduced for ranching in the 1970's. Thus, this study genetically compares the spawning Chinook salmon populations in Petrohué River with those from known salmon farming sites to determine whether or not they originated from escaped individuals.