Microsatellite loci can be used to estimate spawning escapements of individual Pacific salmon populations returning to remote spawning locations throughout large river systems by analysis of appropriately weighted samples from test fisheries near the river mouth. Variation at six microsatellite loci was surveyed from approximately 1,700 sockeye salmon (Oncorhynchus nerka) from 17 populations in the Skeena River drainage in northern British Columbia, as well as from 1,400 fish in test fisheries conducted in the lower river during 1996-1999. Simulated mixed-stock samples suggested that the six microsatellite DNA loci should enable relatively accurate and precise estimates of stock composition when utilized for fishery management applications within the river. We also compared the population structure of sockeye salmon from both the Skeena and Nass rivers. Simulated and actual mixed-stock samples suggested that accurate estimates of stock composition of sockeye salmon from these two major production areas in northern British Columbia should be obtained in analysis of samples from mixed-stock marine fisheries.