Walleye (Sander vitreus) stocks in Nipigon Bay and Black Bay historically numbered as the largest stocks in Lake Superior, but collapsed in the 1960s due to overfishing, habitat loss, and other pressures. We used microsatellite DNA analyses to assess the success and relative contributions of past rehabilitation stocking to walleye in Nipigon Bay, and to investigate the relationship between historical and contemporary populations in Black Bay. Based on the genetic data, juvenile stocking and adult transfers from four source populations into Nipigon Bay differed substantially in their contributions to the reestablished population. The genetic data also indicated that natural reproduction was occurring and identified survivors from the former Nipigon Bay population. Similar genetic analysis of scale samples from the historical Black Bay fishery and present-day walleye from a major tributary (Black Sturgeon River) showed that the historical and contemporary samples comprise one genetic stock, which is significantly different from neighboring native and introduced populations. These findings suggest that walleye restoration efforts in Lake Superior are working, and highlight the utility of and options for adaptive management approaches for restoring extirpated populations.