The objectives of the present study were to analyze the variation at 14 microsatellite loci and 1 MHC locus in Nass River, Skeena River, and Southeast Alaska sockeye salmon populations so as to evaluate the suite of loci for application to stock identification. These loci were then applied to the practical issue of estimating the stock compositions in two fisheries, one in Southeast Alaska (where populations from a number of areas could contribute to the fishery) and one in northern British Columbia (where, given the location at the mouth of Portland Inlet, Nass River sockeye salmon would be expected to dominate the catch).