In Lake Nabugabo, Uganda, a satellite of Lake Victoria, approximately 50% of the indigenous fishes disappeared from the open waters subsequent to the establishment of the introduced predatory Nile perch, Lates niloticus. This pattern is similar to the faunal loss experienced in the much larger Lake Victoria. Several of these species persisted in wetland refugia (e.g. ecotonal wetlands, swamp lagoons); however, deep swamp refugia (habitats lying well within the dense interior of fringing wetlands), are available only to a subset of the basin fauna with extreme tolerance to hypoxia. Although air-breathers are common in deep swamp refugia; we also documented a surprisingly high richness and abundance of non-air-breathing fishes. We describe several mechanisms that may facilitate survival in deep swamp refugia including high hemoglobin concentration, high hematocrit, large gill surface area and a low critical oxygen tension (P(c)). In addition, swamp-dwelling fishes showed lower PO(2) thresholds for onset of aquatic surface respiration than the lake-dwelling fishes. This suggests higher tolerance to hypoxia in the swamp fishes because they are able to withstand a lower oxygen tension before approaching the surface. We suggest that physiological refugia may be important in modulating the impact of Nile perch and indigenous fishes in the Lake Nabugabo region; this highlights the need to evaluate relative tolerance of introduced predators and indigenous prey to environmental stressors.