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Predatory alien fishes have been widely introduced into streams in the Cape Floristic Region (CFR), South Africa, but little is known about their effect on native fishes. Results from this 2006 study suggest that the presence of alien predatory largemouth bass, Micropterus salmoides, may have influenced abundance and habitat selection of the native Galaxias zebratus at one location in a small CFR mountain stream. Numbers of adults, but not of juveniles, were significantly lower where M. salmoides was present, suggesting a size-specific influence on G. zebratus abundance. Because other studies have found the influence of a predator to be affected by prey size and the diel activity of predator and prey, we measured microhabitat use by adult and juvenile G. zebratus by day and by night. Galaxias zebratus selected deeper, faster-flowing microhabitats more strongly where M. salmoides was present than where it was absent. This suggests that G. zebratus adjusts its habitat use in the presence of M. salmoides, although differences in available habitat, or in interactions with other indigenous species, could be partly responsible for the observed differences. In-stream vegetation presence was strongly positively related to depth and strongly negatively related to velocity at positions where G. zebratus was observed, suggesting that the deeper, slower-flowing microhabitats occupied by G. zebratus were structurally more complex than the shallower, faster-flowing ones.