The Stikine and Taku rivers in Southeast Alaska (SEAK) support Chinook salmon runs important for various commercial, aboriginal, and recreational fisheries in both the United States (U.S.) and Canada. Included in these are U.S. commercial gillnet fisheries in Alaskan Districts 108 and 111, as well as sport fisheries near Wrangell, Petersburg, and Juneau. U.S. fisheries in these areas harvest stocks of Chinook salmon bound for SEAK and for tributaries in the transboundary Stikine and Taku rivers. Catches of Stikine and Taku river Chinook salmon stocks are subject to a harvest sharing agreement, in which the U.S. and Canada are each given an Allowable Catch specified by the Pacific Salmon Commission, and this relies on catch, escapement, recruitment information, and stock composition estimates to forecast indices of abundance. Until recently, stock composition of harvests was estimated primarily using coded-wire tags, which provided good estimates for marked stocks. However, expansions of these estimates could be uncertain due to a lack of coded-wire tags on all stocks contributing to the fishery, incomplete tagging of index stocks, and in some instances poor estimates of escapement or terminal run size. Genetic stock identification (GSI) provides a complementary set of accurate and reliable stock composition estimates necessary to meet the directives of abundance-based management of Chinook salmon, and is currently used to recalculate actual contributions of above-border Stikine and Taku Chinook salmon to the Districts 108 and 111 sport and commercial fisheries.