Genetic structure of a species should conform, in part, to environmental structure. Three polymorphic enzyme loci in the amphipod Gammarus minus Say are geographically differentiated in gene frequencies in the mid-Appalachian Mountains of the eastern United States, and genetic breaks usually coincide with topographical features and stream divides. Considering alleles as migrational markers, it is expected that heterozygosity would decrease upstream in isolated drainage basins, increase in the headwaters of adjacent but oppositely flowing streams in which gene exchange was occurring between genetically differentiated populations, and increase in sites near regional master streams. These genetic patterns were found to exist in an area near the Juniata River in central Pennsylvania.