Niche-based hypotheses have been proposed to explain processes and mechanisms of success in the establishment of non-native species into native communities. Competition due to niche overlap may lead to native species niche shift and to native species replacement. To understand the ecological consequences of trophic interactions between non-native rainbow trout and native and endangered marble trout, we used as model system the Idrijca river (Western Slovenia) in which marble trout occurs either in allopatry (MTa) or in sympatry (MTs) with rainbow trout (RTs). We focused on different metrics of niche change such as centroid shift, niche overlap and trophic niche breadth using stable isotope analysis (δ15N and δ13C). Our results showed plasticity in niche overlap between MTs and RTs and niche shift of marble trout when occurring in sympatry with RTs, but not due to a niche replacement of MTs by RTs. Niche breadth of marble trout increases in sympatry and the trophic position during the growth period was higher for MTs than MTa.