The effectiveness of pelvic fin ray microchemistry of muskellunge, Esox masquinongy Mitchill, to identify stocked individuals along with the potential to identify naturally reproduced fish were evaluated. Fish and water samples were obtained from one hatchery and seven lakes with natural differences in water Sr:Ca to determine whether location-specific environmental signatures were recorded in sectioned muskellunge pelvic fin rays, including fish of known environmental history. Water and fin ray Sr:Ca were strongly correlated. Six lakes in Illinois possessed Sr:Ca signatures that were distinct from the hatchery where muskellunge were raised, resulting in pronounced shifts in Sr:Ca across sectioned fin rays of stocked fish. Hatchery and lake-specific Sr:Ca signatures were stable across years. Sixteen of 19 individual fish known to have been stocked based on PIT tags implanted at stocking were correctly identified as hatchery-origin fish using fin ray core Sr:Ca. Results also indicated that the hatchery Sr:Ca signal can be retained for at least 7 years in fin rays of stocked fish. Fin ray microchemistry is a non-lethal approach for determining environmental history of muskellunge that could be used to assess movement patterns in lake and river systems and the degree to which muskellunge populations are supported by natural reproduction and stocking.