Seven hatchery populations and seven of eight wild populations of brook trout sampled were polymorphic for both the LDH-B and the transferrin loci. The degree of variations of allele frequencies as well as of the amount of heterozygosity was generally greater among hatchery fish than those from natural populations. Calculations of interpopulation heterogeneities of allele frequency differences permitted distinguishing all of the hatchery strains, but not all of the small wild populations, from each other. While gross intra-population heterogeneity was found, an assessment of the breeding structure of wild brook trout in a stream was not possible.