Many small, isolated north temperate waterbodies experience hypoxic conditions and winterkill events. Although such waterbodies are found in the natural ranges of two congeneric sunfishes (pumpkinseed, Lepomis gibbosus and bluegill, L. macrochirus), many contain pumpkinseed but no bluegill; a biogeographic pattern that has remained unexplained. To test whether a greater hypoxia tolerance in pumpkinseeds could explain these differences in distribution, we conducted hypoxia tolerance trials by subjecting each species to declining oxygen concentrations over ca. 16 h in aquaria. We also measured the activities of key metabolic enzymes in the muscle of wild individuals. Pumpkinseeds showed significantly higher tolerance to hypoxic stress than bluegills, as indicated by dissolved oxygen concentration at the time of equilibrium loss. Consistent with this result, white muscle from pumpkinseed had higher levels of lactate dehydrogenase, a marker enzyme for anaerobic capacity. There was no difference between species in the activity level of pyruvate kinase, suggesting that pumpkinseed do not display a general upregulation of glycolysis, but rather an upregulation of anaerobic capacity. Our results support the hypothesis that evolved differences in winter hypoxia tolerance can act as a macrohabitat partitioning mechanism in North American sunfishes.