<p>The consumption of thiaminase can cause thiamine deficiency, which has been hypothesized to impede reintroduction efforts of lake trout (<i>Salvelinus namaycush</i>). In fishes, consumption of thiaminase is hypothesized to affect swimming performance and morphology because thiamine deficiency manifests as cardiac and neurological impairments. However, how those effects may differ among populations with different historical exposures to thiaminase remain understudied, despite the importance of these traits to survival and fitness. Here, juvenile lake trout from strains that originated from Seneca Lake and Slate Islands were reared in a common garden environment and received either an experimental diet containing thiaminase or a control diet. Two hundred and sixty days after the initiation of the diets, critical swim speed, morphology, and colouration were compared between strains and diets. Results indicated that, regardless of strain, the diet containing thiaminase negatively affected critical swim speed, decreased ventral-dorsal depth, and increased yellow pigmentation. While most of the negative effects of the thiaminase diet did not differ between the two strains, an increase in red pigmentation was observed in Seneca Lake fish that had received the thiaminase diet. We discuss how strain selection could help mitigate effects of thiaminase exposure on the success of reintroduction efforts for lake trout.</p>