Natal philopatry in lake sturgeon (Acipenser fulvescens) has been hypothesized to be an important factor that has lead to genetically distinct Great Lakes populations. Due to declining abundance, population extirpation, and restricted distribution, hatchery supplementation is being used to augment natural recruitment and to reestablish populations. If hatchery-reared lake sturgeon are more likely to stray than naturally produced individuals, as documented in other well-studied species, outbreeding could potentially jeopardize beneficial site-specific phenotypic and genotypic adaptations. From 1983 to 1994, lake sturgeon propagated using eggs taken from Lake Winnebago adults (Lake Michigan basin) were released in the St. Louis River estuary in western Lake Superior. Our objective was to determine whether these introduced individuals have strayed into annual spawning runs in the Sturgeon River, Michigan. Additionally, we estimated a natural migration rate between the Sturgeon River and Bad River, Wisconsin populations. Presumed primiparous lake sturgeon sampled during Sturgeon River spawning runs from 2003 to 2008 were genotyped at 12 microsatellite loci. Genotypic baselines established for the Sturgeon River (n = 101), Bad River (n = 40), and Lake Winnebago river system (n = 73) revealed a relatively high level of genetic divergence among populations (mean F_ST = 0.103; mean R_ST = 0.124). Likelihood-based assignment tests indicated no straying of stocked Lake Winnebago strain lake sturgeon from the St. Louis River into the Sturgeon River spawning population. One presumed primiparous Sturgeon River individual likely originated from the Bad River population. Four firstgeneration migrants were detected in the Sturgeon River baseline, indicating an estimated 3.5% natural migration rate for the system.