AbstractPhysiological features of species can determine the resilience and adaptation of organisms to the environment. Swimming capacity and metabolic traits are key factors for fish survival, mating and predator–prey interactions. Individuals of the same species can display high phenotypic variation often in response to varying environmental conditions. We investigated the effects of captive breeding conditions on swimming capacity, metabolic traits and morphology by comparing a captive population with a wild population of the endangered Spanish toothcarp (Aphanius iberus). We measured swimming capabilities and oxygen‐uptake rates simultaneously, the latter as a proxy for metabolic rate, using a swim tunnel respirometer. Results showed significant differences in standard metabolic rate (SMR), maximum metabolic rate (MMR) and absolute aerobic scope (AAS) between populations, as well as differences in morphological features between populations and sexes. In contrast, we did not find significant differences in critical swimming speed between populations or sexes. Differences in SMR between sexes were found in the captive population, and males showed nearly a twofold increase in SMR when compared with females. SMR, MMR and AAS were, on average, twofold lower for the captive population in comparison with the wild population. These differences in metabolic traits likely reflected captivity conditions, which were low food availability and the absence of predators, which in turn, may have influenced morphological traits, such as body and caudal peduncle shape and head size. At the same time, morphological traits also influenced metabolic traits of the populations. The lower SMR and MMR of captive individuals may be related to their deeper body shapes. Taken together, our results suggested that captive breeding conditions caused significant physiological and morphological changes in the endangered Spanish toothcarp. Reduced metabolic traits and changes in morphology may affect fitness‐related traits of the captive populations once reintroduced into the wild, thereby compromising conservation efforts. We therefore recommend to experimentally testing for the effects and consequences of captive breeding conditions before fish are released into the wild for successful conservation of them and other endangered species.