The length and mass ratio, diet and isotopic composition of Aplochiton zebra and Aplochiton taeniatus inhabiting a Salmo trutta-invaded and a S. trutta-free lake in southern Patagonia were compared. Results indicate that S. trutta exercises important trophic interference over A. zebra and A. taeniatus, causing changes in their dietary composition by reducing the consumption of winged Diptera through changes in feeding behaviours that involve jumping out of the water. This effect is significantly higher in A. zebra than in A. taeniatus a species that has a highly specialized diet. The dietary changes of A. zebra and A. taeniatus in sympatry with S. trutta lead to an impoverishment of their isotopic nitrogen signals (δ15N), suggesting a reduction of their trophic position. In the case of A. zebra, this translates into a significant decrease in its body condition factor. Such interference could lead to a population decline of this species and would explain the current distribution range decline and allopatry with S. trutta in fluvial systems.