Determination of run timing is an important component of salmonid fisheries management and was the major focus of this study. Population structure of Sockeye Salmon Oncorhynchus nerka was examined in the Skeena River in northern British Columbia. Variation at 14 microsatellites was surveyed for 27 populations in the drainage. There were 9,473 individuals sampled in a lower river test fishery during 2000–2011 in order to provide information on relative abundance and arrival time for specific populations near the mouth of the river. Within-lake or within-river tributary structuring of populations was the general pattern observed, with 10 populations from Babine Lake clustering together in 91% of the dendrograms evaluated, and two populations from Lakelse Lake clustering together in 100% of the dendrograms evaluated. The 27 populations sampled were arranged in 12 reporting groups for genetic stock identification applications. The estimated stock composition of known-origin mixtures was within 2% of the correct estimate for all 12 reporting groups present in the mixtures. Sockeye Salmon typically began arriving at the test fishery on the lower Skeena River by June 10, peaking in daily abundance in late July or early August, and finished migrating past the test fishery by mid-September. Relative timing of the 12 reporting groups, from earliest to latest, was as follows: Lakelse Lake, Alastair Lake, Zymoetz River, Morice Lake, Kispiox River, Sustut Lake, Babine Lake, Slamgeesh Lake, Motase Lake, Bear Lake, Kitsumkalum Lake, and Kitwanga Lake. Genetic mixed-stock analysis, coupled with a test fishery in the lower river, can assist managers in regulating fisheries directed at Skeena River Sockeye Salmon.