Recent reviews have further documented the decline of the shortjaw cisco Coregonus zenithicus in Lake Superior. This fish was the most abundant deepwater cisco species in Lake Superior in the early 1920s but presently makes up less than 1% of all deepwater ciscoes (i.e., including shortjaw cisco, bloater C. hoyi, and kiyi C. kiyi) captured in biological surveys. Directed overfishing of deepwater cisco species during the 1930s and again during the mid-1960s and 1970s has been suggested as the cause of the shortjaw cisco's demise. In this paper, we re-examined the overfishing hypothesis by using historical and recent survey data to estimate the proportion of the historical commercial fishery landings that comprised shortjaw ciscoes. We developed time series of estimated harvest and relative abundance for all statistical districts in Michigan waters of Lake Superior during 1929–1996, for which aggregate catch and effort data were available but not previously examined. The spatial distribution of the fishery and the relationships of catch to fishing effort were examined for evidence of overfishing. Our analysis suggested that directed overfishing was probably not the cause of shortjaw cisco demise, as this species appeared to be declining in all statistical districts regardless of the intensity of the fishery. A count-based population viability analysis indicated that quasi-extinction of the shortjaw cisco is highly probable in the near future. We propose an alternative hypothesis based on the decline of Lake Superior's keystone predator, the lake trout Salvelinus namaycush, which resulted in an expansion of the population of its principal prey, the cisco C. artedi, due to release from predation pressure. Competitive or predation interactions between the cisco and shortjaw cisco may be more likely explanations for the demise of the latter species.