Technical Abstract: Genetic variation fuels selective change in natural and captive populations. In establishing a broodstock for selective improvement the degree of genetic diversity is an important consideration because it provides an indication of the scope for selective progress. Here three strains of rainbow trout with a history of domestication were examined for genetic variation in terms of heterozygosity and allelic diversity at nine polymorphic microsatellite loci. The average heterozygosity was 71.5% at these nine loci, which had an average of 14 alleles per locus. Each locus was represented by alleles unique to at least two of the three strains. Measures of population differentiation, FST, and non-random breeding, FIS, were significant, and provide additional evidence of unique genetic variation present in each strain. The variation present between these strains suggests that crosses within and among these groups will be useful for identifying informative genetic marker loci and associations between markers and quantitative traits. Furthermore the variation contributed by each population suggests there is greater scope for selective improvement of numerous traits within a synthetic strain combining these three strains, than within any individual strain.