Eleven microsatellite DNA loci were identified and characterized for Atlantic salmon (Salmo salar) collected from the Penobscot River, Maine, USA and the River Nith, Scotland, UK. The markers revealed high levels of genetic diversity (seven to 48 alleles per locus), heterozygosity (to 100%), and allelic heterogeneity (all comparisons). Considerable differentiation was observed as the genetic distance (chord) between the two collections was 0.680 and the pairwise FST, 0.12, was highly significant. These findings are consistent with patterns of continental-level differentiation observed previously using an alternate suite of microsatellite loci. Locus-by-locus analyses of molecular variance suggested that most markers were suitable for delineating kinships and population genetic structure.