This study quantified and compared hypoxia tolerance and swim performance among cyprinid fish species from rapid-, slow-and intermediate-flow habitats (four species per habitat) in China. In addition, we explored the effects of short-term acclimation on swim performance, maximum metabolic rate (Ṁ O2,max ) and gill remodelling to detect habitat-associated patterns of plastic response to hypoxia. Indices of hypoxia tolerance included oxygen threshold for loss of equilibrium (LOE 50 ) and aquatic surface respiration (ASR 50 ), and critical oxygen tension for routine metabolic rate (P crit ). Critical swimming speed (U crit ) and Ṁ O2,max were measured under normoxic and hypoxic conditions after 48 h acclimation to normoxia and hypoxia, and gill remodelling was estimated after 48 h of hypoxia exposure. Both traditional ANCOVA and phylogenetically independent contrast (PDANOVA) analyses showed that fish species from rapidflow habitats exhibited lower LOE 50 compared with fish from intermediate-and slow-flow habitats. Habitat-specific differences in P crit and U crit were detected using PDANOVA but not traditional ANCOVA analyses, with fish species from rapid-flow habitats exhibiting lower P crit but higher U crit values compared with fish from intermediate-and slow-flow habitats. Fish species from rapid-flow habitats were also characterized by less plasticity in swim performance and gill morphology in response to hypoxia acclimation compared with species from slow-flow habitats, but a greater drop in swim performance in response to acute hypoxia exposure. The study detected a habitat-specific difference in hypoxia tolerance, swimming performance and its plasticity among fish from habitats with different flow conditions, possibly because of the long-term adaptation to the habitat caused by selection stress. The PDANOVA analyses were more powerful than traditional statistical analyses according to the habitat effects in both hypoxia tolerance and swimming performance in this study.