The combined stresses of fasting and hypoxia are common events during the life history of freshwater fish species. Hypoxia tolerance is vital for survival in aquatic environments, which requires organisms to down-regulate their maintenance energetic expenditure while simultaneously preserving physiological features such as oxygen supply capacity under conditions of food deprivation. Generally, infrequent-feeding species who commonly experience food shortages might evolve more adaptive strategies to cope with food deprivation than frequent-feeding species. Thus, the present study aimed to test whether the response of hypoxia tolerance in fish to short-term fasting (2 weeks) varied with different foraging modes. Fasting resulted in similar decreases in maintenance energetic expenditure and similar decreases in Pcrit and Ploe between fishes with different foraging modes, whereas it resulted in decreased oxygen supply capacity only in frequent-feeding fishes. Furthermore, independent of foraging mode, fasting decreased Pcrit and Ploe in all Cypriniformes and Siluriformes species but not in Perciformes species. The mechanism for decreased Pcrit and Ploe in Cypriniformes and Siluriformes species is at least partially due to the downregulated metabolic demand and/or the maintenance of a high oxygen supply capacity while fasting. The present study found that the effect of fasting on hypoxia tolerance depends upon phylogeny in freshwater fish species. The information acquired in the present study is highly valuable in aquaculture industries and can be used for species conservation in the field.