The Northern-Central Adriatic Sea is one of the most productive areas of the Mediterranean Sea supporting a broad diversity of habitats. A high variety of fishing activities have exploited the Adriatic Sea for centuries leading to the depletion of key demersal species. Within this species rich basin, the Pomo Pit (also called Jabuka Pit, 200-260 m of depth) is one of the most important habitats for some shared demersal stocks of the Adriatic Sea and its physical and oceanographic characteristics support the presence of Essential Fish Habitats. In addition, the Pomo Pit is also an important spawning/nursery area for many demersal species and in particular for the stock of European hake in the Northern and Central Adriatic. In this study we applied a metabarcoding approach to study the feeding habits of European hakes sampled within the Pomo Pit and to compare this feeding behaviour to the diet of hakes caught outside the Pomo area. Our analyses proved the presence of specific niche partitioning and food preferences between hakes living inside and outside the Pomo Pit and confirmed the ontogenetic shift from a diet based mainly on crustacean to a more piscivorous feeding behaviour in adult fish. These results for the first time highlighted the crucial role played by the Pomo Pit in M. merluccius feeding behaviour and ontogenetic development strengthening the hypothesis of the presence of an Essential Fish Habitat and promoting a careful management of this ecosystem through focused conservation measures.