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Abstract The practice of mitigating cannibalism in aquaculture is an important focus for hatcheries seeking to maximize yield and has been maintained in hatcheries focusing on wild stock restoration. We hypothesize, however, that a cannibal feeding strategy may confer performance advantages over a non-cannibal feeding strategy and that perhaps cannibal size grading may not be optimal for hatcheries focusing on conservation goals. This study examined metabolic performance differences between cannibal and non-cannibal burbot, Lota lota maculosa, at the Kootenai Tribe of Idaho Twin Rivers Hatchery in Moyie Springs, ID, USA. After habitat alteration led to functional extinction of burbot in the region, the Twin Rivers Hatchery has played a leading role in the reestablishment of burbot in the Kootenai River, ID, and British Columbia. We examined morphometric data (weight, length and condition factor), whole animal resting metabolic rate and the enzyme activity of lactate dehydrogenase, citrate synthase and 3-hydroxyacyl-CoA dehydrogenase to describe the baseline metabolic performance of cannibal and non-cannibal burbot. Taken together, our results demonstrated significant differences in the metabolic strategies of cannibal vs. non-cannibal burbot, where cannibals relied more heavily on carbohydrate metabolism and non-cannibals relied more heavily on glycolytic and lipid metabolism. This study demonstrates the need to reevaluate the traditional practice of removing cannibal fish in conservation hatcheries, as it may not be the ideal strategy of raising the most robust individuals for release. When natural habitat conditions cannot be restored due to permanent habitat alteration, prioritizing release of higher performing individuals could help achieve conservation goals.