To test whether patches of papyrus swamp contribute to diversification of populations of non-air-breathing fishes, the gill morphology ofBarbus neumayeriwas compared between a papyrus swamp and several tributaries which differed in oxygen regime. Total gill filament length differed among sites and was negatively related to dissolved oxygen availability, supporting strong selection pressure for low-oxygen tolerance in the swamp interior. Among recaptures of markedB. neumayeriover a 4.5-year period among the focal swamp and connected stream and river sites, 93% of fish were recovered at the site of capture. Some of the individuals that moved crossed physicochemical gradients and traversed long distances within the swamp/stream system. This movement rate would theoretically be sufficient to homogenize gene frequencies among populations. However, randomly amplified polymorphic DNA (RAPD) markers indicated significant genetic differentiation among sites and no relationship between genetic differences and geographical distances among sites suggesting habitat-specific selection pressures on dispersers, rather than insufficient dispersal.