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The Government of Canada is considering a recommendation by the Committee on the Status of Endangered Wildlife in Canada to list shortjaw cisco (Coregonus zenithicus) as “Threatened” throughout its range under the Species At Risk Act (SARA). If the listing is approved, shortjaw cisco will receive legal protection, including protection for its ‘critical habitat.’ This study focused on habitat characteristics associated with specimens identified as shortjaw cisco collected with targeted sampling in Lake Huron of the Laurentian Great Lakes. Competing habitat-use models were developed using available data for three physical habitat variables: Water Depth, Substrate Slope, and Cliff Distance, and the models were evaluated using binary logistic regression and ranking of Akaike information criteria. For the habitat factors examined, Water Depth was the most important variable for explaining the observed distribution of identified shortjaw cisco, although this factor alone was not sufficient to adequately represent habitat for this taxonomically uncertain and rare animal. Future habitat discrimination for this hypothesized species at risk must be based on (a) reduction of taxonomic uncertainty, (b) expansion of sampling effort, and (c) consideration of additional physical and ecological habitat factors. [ABSTRACT FROM AUTHOR]