Temperature has a major impact on the physiological processes of freshwater invertebrates. Despite the endangered status of many freshwater mussel species and the potential effect of global warming on North America’s northern aquatic habitats, thermal sensitivity of the metabolic apparatus of freshwater bivalves has received little attention. By examining the thermal sensitivity of 10 key metabolic enzymes and in situ growth rates of latitudinally separated populations (temperate and subarctic) of two closely-related Pyganodon species from northeastern North America, we provide the first insights into thermal sensitivity of key enzymes of energy and reactive oxygen species metabolism in relation to habitat localization and growth performance. The subarctic population of Pyganodon grandis displayed higher in situ growth rates than the temperate population of Pyganodon fragilis. The subarctic population of P. grandis had a lower mitochondrial capacity as expressed by citrate synthase and cytochrome c oxidase but displayed similar electron transport system (ETS) and higher isocitrate dehydrogenase capacities. Our results suggest that higher growth performance of the subarctic population of P. grandis is not associated with higher aerobic capacity. The high thermal sensitivity of mitochondrial enzymes in subarctic population of P. grandis might rather reflect enhanced stenothermy. The higher electron transport system/cytochrome c oxidase ratio for the subarctic P. grandis species than P. fragilis might affect mitochondrial regulation or reactive oxygen species production. Antioxidant enzymes displayed lower Q10s suggesting thermal independence of antioxidant capacity.