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The Berg–Breede River whitefish, Barbus andrewi, an endangered Cape Floristic Region endemic, was once widespread in both the Berg and Breede River catchments. However, its distribution has been strongly reduced, apparently by human-related activities, over the last century, and the Hex River now contains one of the last recruiting populations within its native range. This population was last surveyed by Christie who found that the species occurred in six pools over a 9-km stretch of the upper Hex River. We re-surveyed fish populations at Christie’s sites in 2015 to evaluate differences in the fish community between 2002 and 2015. Our data indicated that the distribution of B. andrewi in the Hex River has declined from six to four pools and that its density in the study area in 2015 (0.57 fish per 100 m2 ± 0.31 fish per 100 m2 ) was more than fivefold lower than that recorded in 2002 (3.39 fish per 100 m2 ± 1.40 fish per 100 m2 ). Moreover, small size classes of B. andrewi (< 10 cm) were largely absent in 2015, indicating recruitment failure in recent years. Habitat degradation, exacerbated by a severe flood in 2008, and recent invasions by predatory non-native fishes (smallmouth bass, Micropterus dolomieu and sharptooth catfish, Clarias gariepinus) are identified as likely causes of this decline. Cape kurper, Sandelia capensis, another native species, was relatively common in 2002 but not recorded in 2015, whereas the density of native Breede River redfin, Pseudobarbus burchelli, was higher in 2015 than in 2002. Urgent conservation actions including managing non-native fish invasions and mitigating agricultural impacts on aquatic habitat are required to prevent further decline, and possible extirpation, of the Hex River population of B. andrewi. Conservation implications: Urgent conservation actions including preventing further increases in the abundance and distribution of non-native fishes, and improving habitat and water quality through mitigating agricultural impacts, are required to prevent further decline, and possible extirpation, of the Hex River population of B. andrewi.