These data describe morphometric (body shape) measurements of wild and artificially reared (i.e., raised in a laboratory or fish hatchery) cisco (Coregonus artedi) from lakes Huron and Ontario in the Laurentian Great Lakes. Specifically, this data release includes traditional morphometric data (i.e., measurements of fish specimens) describing wild and artificially reared cisco from Lake Huron, as well as geometric morphometric data (i.e., landmarks placed on images of fish) describing cisco head shapes for wild and artificially reared cisco from both lakes Huron and Ontario. Artificially reared individuals from Lake Huron were raised at the U.S. Geological Survey Great Lakes Science Center in Ann Arbor, MI, USA, and one family of offspring were split among three rearing temperature treatments. Artificially reared individuals from Lake Ontario were raised at the Tunison Laboratory of Aquatic Science in Cortland, NY, USA. These data were collected by the authors on this data release from 2017-2023 and used to analyze the impacts of artificial rearing on cisco body shapes, with a focus on head shapes.