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This study finds that non-native species and warming temperatures have significant negative effects on Arctic char Salvelinus alpinus abundance in Irish lakes. Eutrophication was not important at the range of total phosphorus tested (0.005-0.023 mg l(-1)). Model results predict that S. alpinus occur across the temperature range sampled (8.2-19.7 degrees C) when non-natives are absent, but S. alpinus catch is predicted to be close to zero irrespective of temperature when non-native catch is high. This result indicates that to persist, S. alpinus may require a habitat where non-natives are at low abundance or absent. Salvelinus alpinus segregated from other species along the thermal axis, inhabiting significantly colder water and actively avoided non-native species, which appeared to limit their distribution. The thermal niche realized by S. alpinus in non-native dominated lakes was thus compressed relative to native dominated lakes and S. alpinus population density was significantly lower. These findings were consistent even when the only non-native present was Perca fluviatilis. Temperature appeared to limit the distribution of non-native species, such that the presence of deep thermal refugia is currently facilitating S. alpinus co-existence with non-natives in associated lakes. Diet analysis identified P. fluviatilis as potential predators and competitors. This study provides strong evidence that non-native species are a key driver of low S. alpinus abundance in Irish lakes. Temperature increases associated with climate change are identified as a secondary concern, as they could erode S. alpinus' thermal niche and lead to their extirpation. The lower thermal buffering capacity of shallow lakes identifies these as higher risk systems. Salvelinus alpinus conservation in Ireland should focus on preventing future illegal non-native species introductions because unlike other stressors (e.g., eutrophication etc.), species introductions are rarely reversible.