The deepwater cisco (Coregonus johannae) was one of the largest ciscoes in the Great Lakes. Its average length was 30 cm (12 inches) and it was about 1.0 kilogram (2.2 pounds) in weight. Occurring only in Lakes Huron and Michigan, and inhabiting waters between 50 and 150 metres deep, it was difficult to distinguish from other ciscoes and was possibly the same species as the shortjaw cisco (Coregonus zenithicus). The deepwater cisco was distinguished by usually having fewer than 33 gill rakers, relatively long pectoral fins, and unpigmented jaws. It was a silvery colour with a pink or purple lustre and a green or blue back. It spawned in August and September, earlier than most other ciscoes. Not much is known about its specific behaviors. Its diet consisted of Mysis relicta, fingernail clams, and various aquatic insects. Because of its large size, the deepwater cisco was heavily fished commercially.

The main reasons for its extinction was a combination of competition from the invasive alewife, predation by the introduced sea lamprey, and commercial fishing on the Great Lakes.