Commercial troll fisheries in Southeast Alaska harvest Chinook salmon originating from Alaska, British Columbia, and the Pacific Northwest. Only individuals larger than 711 mm may be retained; smaller individuals must be released. Encounters with sublegal-sized Chinook are not recorded and the subsequent mortality is unknown. Beginning in 1998, studies were conducted to estimate the rate at which sublegal-sized Chinook salmon are incidentally caught by this fishery. As part of these studies tissue samples were taken from sublegal-sized individuals for mixed stock analyses using genetic information. The estimation of stock composition of the samples taken during the 1998–2003 summer troll fisheries is described in this report. The Upper Columbia River(Summer, Fall)/Snake River (Fall), Southern Southeast Alaska, and Strait of Georgia were consistently the largest contributors to the annual sublegal incidental encounters. Results indicate considerable variation in the composition of sublegal-sized individuals encountered by troll fishers within years, but consistent patterns of composition by major groups across years.