In Wisconsin, muskellunge Esox masquinongy have been propagated for over 70 years as part of a comprehensive management plan to provide angling opportunities and develop trophy fisheries. However, more recently concerns exist regarding the genetic integrity and long-term viability of the Wisconsin Department of Natural Resources’ (WDNR) propagation program. To address these concerns, starting in 2005, the WDNR muskellunge propagation program underwent a series of strategic modifications aimed at protecting the contemporary genetic integrity of populations and ensuring the long-term sustainability of muskellunge. Following implementation a critical evaluation to determine how successful these new genetic broodstock guidelines have been at maintaining genetic diversity and effective population size (Ne) of stocked muskellunge is critical. Additionally, from a conservation genetics standpoint, it is critical to identify at what life stages, if any, bottlenecks in genetic diversity are occurring.