The hierarchical genetic structure of aquatic organisms is highly influenced by watershed boundaries or other key geological features. Previous genetic research on walleye (Sander vitreus) and muskellunge (Esox masquinongy) across their native range in Wisconsin showed sampled populations in the Upper Chippewa River (UCR) watershed were more similar to fish from the neighboring Upper Wisconsin River (UWR) watershed than they were to fish in the lower reaches of the Chippewa River watershed. The disjunct is likely the result of glacial processes or widespread, cross-boundary stocking. The underlying cause is important in implementing stock-based management of coolwater game fish in Wisconsin. Our objective was to determine if the disjunct in watershed genetic structure was consistent with non-propagated fish species and thus, likely the result of natural (geological) processes. The genetic structure of rock bass (Ambloplites rupestris) and johnny darters (Etheostoma nigrum) was determined by sampling >15 populations for both species across northern Wisconsin with special emphasis on subwatersheds bordering the watershed boundary of the UWR and UCR. Genetic diversity was assessed at ≥12 loci for each species and genetic structure of each species was predicted using standard methods. Based on data collected to date, genetic structure of both species was consistent with contemporary watershed boundaries. Assuming these species represent non-propagated coolwater fish genetic structure, these data suggest walleye and muskellunge structure has been influenced by past propagation. Efforts to effectively conserve contemporary genetic diversity should consider this disjunct and the risks associated with considering contemporary versus historical patterns of diversity.