Coregonus artedi (Cisco) and Coregonus clupeaformis (Lake Whitefish) are coldwater fishes native to some inland lakes in Wisconsin. We conducted a statewide assessment of Cisco and Lake Whitefish status using experimental-mesh vertical gillnets during the summers of 2011–2014. Cisco and Lake Whitefish relative abundances varied from 0 to 137 and 0 to 3 fish/net night, respectively. About 29% of the Cisco and 33% of the Lake Whitefish populations were potentially extirpated from inland lakes in Wisconsin; most potential extirpations were from southern Wisconsin, but extirpations occurred statewide. Invasive species, climate change, land-use change, and excess nutrient loading may have contributed to causing extirpations of Cisco and Lake Whitefish. Conservation of remaining populations of Cisco and Lake Whitefish will require efforts to minimize these perturbations.