The invasion of Indo-Pacific fish through the Suez Canal has dramatically altered the diversity of fish assemblages on the upper shelf of the southeastern Mediterranean. Yet, their role in the trophodynamics of the novel assemblages has been largely overlooked. In the present study, we investigated the impacts of the alien fish species on the structure of the food web along the Israeli upper shelf soft bottoms, as expressed by their biomass relative abundance, and by comparing the mean and distribution patterns of the trophic levels among the aliens and the local native species. Our study, based on examination of more than 200,000 fishes belonging to 111 species, revealed that at 20-m alien species comprised 54 % of all sampled individuals while comprising 70 % of the biomass; at 40 the alien species comprised 67 % of all sampled individuals and 45 % of the biomass. Overall, the mean weighted trophic level of the aliens was 3.74, while that of the natives was 3.39. Depth was found as an important factor affecting the trophic levels of both native and alien species. At a depth of 20 m, the combined mean weighted trophic level (natives + aliens) was slightly higher than at 40 m (3.61 and 3.56, respectively), although depth impact differed between aliens and natives. Between a depth of 20 and 40 m, the mean weighted trophic level of aliens increased from 3.65 to 3.85, while that of the natives decreased from 3.54 to 3.33. These findings indicate that the local food webs have gone through significant modification, with a trend of increasing dominance of alien fish.