Significant heterogeneity was found for allelic variation at eight protein loci among Atlantic salmon (Salmo salar) from tributaries in the Kyles of Sutherland river system in northeast Scotland. Differentiation at the mMEP-2∗ locus was greatest and correlated with summer water temperature as found in other studies. This supports the contention that the polymorphism is affected by selection. Indirect estimates of gene flow among tributary populations based on Ncm, the effective number of individuals exchanged between tributary populatuons, and calculated from Wright's FST were 6.2 for mMEP-2∗ and varied from 9.3 to 79.8 for the other loci. The overall mean estimate was 15.1. An estimate of Ncm based on the mean frequency of “private” alleles was 2.0. The proportion of migrant salmon among each tributary's breeding population is likely to be in the order of 5% or less. The genetic substructuring of the Atlantic salmon observed within the river system provides the scope for genetic adaptation of populations to local environmental conditions.