The exploitation of fishery resources acts as a driving force on cetaceans both directly, by determining their fishing mortality or injury as by-catch species, and indirectly, through the lowering the availability of their prey. This competitive overlap between fishing and cetaceans often results in inadequate solutions so that in some cases there have been cases of intentional cetacean culling to maximize fishing production. A modelling approach applied to investigate the ecological roles of cetaceans in the food web could prove more effective to integrate ecological and fishing aspects and to provide suggestions for management. The comparative analysis carried out in the Gulf of Taranto (Northern Ionian Sea, Central Mediterranean Sea) showed that fishing exploitation provides impacts on the investigated food web greater than those due to cetacean predation. Trawling was estimated to be the most negatively impacting fishing gear considering the mortality rates and consumption flows. On the other hand, the striped dolphin was the main impact on the food web due to its highest consumption flows. Analysis showed a negative and non-selective impact on the exploited species due to the fishing gears, while the odontocetes proved to select their prey species and provide a positive impact in the assemblage. In particular, while the fishing gears are primarily size selective, targeting mostly large and economically valuable fish, the odontocetes seem to follow a co-evolution process with their prey, developing a specialization in their resources, providing control of the meso-consumers and ensuring a trophic stability in the ecosystem.