Competition with a non-native species can lead to morphological changes in native organisms induced by phenotypic plasticity, and by selection against individuals that do not adjust their morphology to the novel selection pressure. The morphological changes in native organisms are often associated with rapid behavioural responses to competition with the invader. However, knowledge of the interaction between the behaviour and morphology of native organisms competing with a non-native species remains scarce. Here, we investigated the effect of competition with non-native brook trout Salvelinus fontinalis on head shape of native brown trout Salmo trutta in a stream system where changes in diet and territorial behaviour of sympatric brown trout have previously been demonstrated. We found that sympatric brown trout had smaller eyes, shorter lower jaws and more terminal mouth than allopatric conspecifics. These differences in head shape were highly repeatable over a period of 12 months. Apparent survival indicated that the selection on head shape of brown trout was weaker in the sympatric than in the allopatric stretch of the stream. The results suggest that these changes reinforce divergences of foraging strategies between the allopatric and sympatric brown trout, which can negatively affect their population dynamics and trophic function in the food-web.