We investigated the effects of helminth endoparasite load on the physiological performance of 2 sympatric fishes, Lepomis macrochirus and Lepomis megalotis (Centrarchidae). Species-specific swimming endurance and thermal tolerance were used as measures of physiological performance. A discriminant function analysis for endurance indicated that only kidney parasite load significantly correlated with the first discriminant function. However, overall increases in parasite load within the mesentery, heart, liver, and small intestine were each associated with observed decreases in endurance for both species. A discriminant function analysis also indicated that increases in mesentery and liver parasite load were significantly correlated with decreases in thermal tolerance. An overall increase in parasite load within the mesentery, heart, liver, small intestine, and spleen was also correlated with decreased thermal tolerance. Thus, our results suggest that helminth endoparasite load may play an important role in the physiological performance of these sympatric fishes. Differences in microhabitat utilization and partitioning of L. macrochirus and L. megalotis correlate with species-specific physiological performance. For example, microhabitats with greater current velocities are used by L. megalotis because of the greater capacity of this species for endurance. However, parasite loads that significantly reduce endurance would force changes in habitat utilization causing direct competition among species normally partitioned. We offer a theoretical discussion of how parasite load may create opportunities for interaction and competition among individuals and species usually partitioned by physiologically based preferences in microhabitat utilization.