Variation at four microsatellite loci, Omy77, Ots100, Ots3, and Ots103, was characterized for three populations of sockeye salmon (Oncorhynchus nerka) found within 50 km of each other in the Barkley Sound region of Southwest Vancouver Island, British Columbia. We used a simple polyacrylamide gel electrophoresis technique to analyze microsatellite alleles amplified from total genomic DNA extracts of liver and archived scales. Classes from several years were examined for each population, with little significant interannual variability detected. Each microsatellite locus was highly polymorphic with 10 alleles at Omy77, 12 alleles at Ots100, 16 alleles at Ots3, and 17 alleles at Ots103; average observed heterozygosities were also high at 75%, 76%, 69%, and 85% respectively. Fst values and pairwise tests indicated that the populations had significantly different allele frequencies, suggesting that the three populations are reproductively isolated. Our results suggested that microsatellite loci can be analyzed with a simple technique to reveal population structure of sockeye salmon on a small geographic scale.