Many inland fisheries are supported by stocking hatchery-produced fish, and fisheries managers often face difficult decisions regarding strain selection. Stocking evaluations that are designed to quantify differences in strain performance provide valuable data for designing stocking programs. Here, we used genetic tools to investigate the capture rate of two strains of Muskellunge that were stocked in Wisconsin lakes. We genotyped a total of 1,011 Muskellunge at 13 microsatellites and used the data from five reference populations to assign fish that were stocked in four Wisconsin lakes to their strain of origin. The strains that were stocked in these lakes were derived from Wisconsin populations in the upper Chippewa River and Wisconsin River drainages and from Leech Lake, Minnesota. The Muskellunge from Leech Lake demonstrated much lower capture rates than the Wisconsin strain, but the results were variable, with a 10% capture rate of fish from the Leech Lake strain in Lake Monona and a 2% capture rate in Lake Wissota, despite similar stocking rates (~25%) in both lakes. We hypothesized that the higher capture rates of Muskellunge from the Wisconsin strain could be due the adaptative advantages of the Wisconsin strain in these waters and suggest that managers continue to stock the nearest native (i.e., Wisconsin) strain to achieve the highest return on investment. Stocking hatchery-produced fish is one of the most common tools employed by fisheries managers to rebuild and sustain inland fisheries (Halverson 2008). One important consideration when building a propagation program is that of choosing appropriate strains that display high survival and growth to maximize the return on stocking investment while also preserving the genetic integrity of