This study evaluated whether the African cyprinid Barbus neumayeri from Rwembaita Swamp (low-oxygen) and Njuguta River (high-oxygen) in the Kibale National Park, Uganda differed in traits related to aerobic and anaerobic metabolic potential. Haematocrit was measured as an index of blood oxygen-carrying capacity, and tissue activities and isozyme composition of lactate dehydrogenase (LDH) were measured as indices of tissue anaerobic capacity. To address whether site-dependent differences were acute responses v. longer-term adjustments to environmental conditions, these variables were measured in fish sampled shortly after collection and after laboratory maintenance under well-aerated conditions. In fish sampled in the field, those from the low-oxygen site had significantly higher haematocrit, but this difference disappeared after long-term laboratory maintenance. In contrast, fish from the low-oxygen site had higher liver LDH activities than fish from the high-oxygen site, and this difference persisted during laboratory maintenance. Polymorphism was detected at both the LDH-A and LDH-B loci, and genotype frequencies for LDH-B differed significantly between collection sites. These results demonstrate physiological, biochemical and genetic differences in B. neumayeri from habitats differing in dissolved oxygen availability and suggest both acute and long-term responses to local environmental conditions.