Oxygen fluctuations are common in freshwater habitats and aquaculture and can impact ecologically and economically important species of fish like cyprinids. To gain insight into the physiological responses to oxygen fluctuations in two common cyprinid species, we evaluated the impact of short-term intermittent hypoxia on oxidative stress and metabolic parameters (including levels of prooxidants and oxidative lesions, antioxidants, mitochondrial enzyme activities, mitochondrial swelling, markers of apoptosis, autophagy and cytotoxicity) in silver carp Hypophthalmichthys molitrix and gibel carp Carassius gibelio. During hypoxia, gibel carp showed higher baseline levels of antioxidants and less pronounced changes in oxidative and metabolic biomarkers in the tissues than silver carp. Reoxygenation led to a strong shift in metabolic and redox-related parameters and tissue damage, indicating high cost of post-hypoxic recovery in both species. Species-specific differences were more strongly associated with oxidative stress status, whereas metabolic indices and nitrosative stress parameters were more relevant to the response to hypoxia-reoxygenation. Overall, regulation of energy metabolism appears more critical than the regulation of antioxidants in the response to oxygen deprivation in the studied species, and further research is needed to establish whether prioritizing metabolic over redox regulation during H/R stress is common in freshwater cyprinids.