Torrent ducks inhabit fast-flowing rivers in the Andes from sea level to altitudes up to 4,500 m. We examined the mitochondrial physiology that facilitates performance over this altitudinal cline by comparing the respiratory capacities of permeabilized fibers, the activities of 16 key metabolic enzymes, and the myoglobin content in muscles between high- and low-altitude populations of this species. Mitochondrial respiratory capacities (assessed using substrates of mitochondrial complexes I, II, and/or IV) were higher in highland ducks in the gastrocnemius muscle – the primary muscle used to support swimming and diving – but were similar between populations in the pectoralis muscle and the left ventricle. The heightened respiratory capacity in the gastrocnemius of highland ducks was associated with elevated activities of cytochrome oxidase, phosphofructokinase, pyruvate kinase, and malate dehydrogenase (MDH). Although respiratory capacities were similar between populations in the other muscles, highland ducks had elevated activities of ATP synthase, lactate dehydrogenase, MDH, hydroxyacyl coA dehydrogenase, and creatine kinase in the left ventricle, and elevated MDH activity and myoglobin content in the pectoralis. Thus, while there was a significant increase in the oxidative capacity of the gastrocnemius that correlates with performance at high altitudes, the variation in metabolic enzyme activities in other muscles not correlated to respiratory capacity, such as the consistent up-regulation of MDH activity, may serve other functions that contribute to success at high altitudes.