Global climate change models indicate that a rise in temperature and reduction in rainfall in the Western Cape Province of South Africa is inevitable and unavoidable. Within the Western Cape lies the Cape Floristic Region (CFR); a biodiversity hotspot with high levels of endemism. This includes its freshwater fish assemblage. Whereas the current greatest threats to native fish biodiversity are habitat degradation and invasion by non-native species, predicted climate change is likely to further impact fish communities negatively. As a master abiotic variable in aquatic ecosystems; temperature influences the fitness, behaviour, and life-histories of aquatic biota. Thermal alteration may therefore affect sensitive fish species. The upper thermal limit, determined via the critical thermal method, has been validated as a measure of thermal sensitivity. To better understand the impacts of climate change on the native fish of the CFR, upper thermal limits (critical thermal maxima/CTmax) were determined for seven native species of freshwater fish. Thermal preferences were also determined for five of these species using the acute gradient tank approach to elucidate thermal habitat preferences. Species that were identified by the IUCN as vulnerable, endangered, or critically endangered were selected from the four main families of native fish in the CFR (Anabantidae, Austroglanidae, Cyprinidae, and Galaxiidae), from four Rivers. Overall, Cape galaxias (Galaxias zebratus), Breede River redfin (Pseudobarbus burchelli), Berg River redfin (Pseudobarbus burgi), Clanwilliam redfin (Pseudobarbus calidus), and fiery redfin (Pseudobarbus phlegethon) were found to be most sensitive to increased temperature (CTmax= 29.8-32.7⁰C). Clanwilliam rock-catfish (Austroglanis gilli) and Cape kurper (Sandelia capensis) were found to be moderately sensitive (CTmax= 33.0-35.3⁰C). Similar trends were found using the thermal preference approach as CTmax and thermal preference were found to correlate well. The results were related to in-situ water temperature, which influenced both parameters. Thermal tolerances and preferences of all the native species exceed that of invasive salmonids (Onchorynchus mykiss and Salmo trutta). However, non-native centrarchids (Micropterus spp.) are more thermally tolerant, indicating an increase in threat by warm adapted non-natives. These data suggest that species interactions and distributions are likely to undergo substantial changes in response to elevated water temperature.