An ecosystem modelling approach was used to understand and assess the Mediterranean marine ecosystem structure and function as a whole. In particular, 2 food web models for the 1950s and 2000s were built to investigate: (1) the main structural and functional characteristics of the Mediterranean food web during these 2 time periods; (2) the key species/functional groups and interactions; (3) the role of fisheries and their impact; and (4) the ecosystem properties of the Mediterranean Sea in comparison with other European regional seas. Our results show that small pelagic fishes, mainly European pilchards and anchovies, prevailed in terms of biomasses and catches during both periods. Large pelagic fishes, sharks and medium pelagic fishes played a key role in the 1950s ecosystem, and have been replaced in more recent years by benthopelagic and benthic cephalopods. Fisheries showed large effects on most living groups of the ecosystem in both time periods. When comparing the Mediterranean results to those of other European regional seas modelling initiatives, the Mediterranean stood alone in relation to the type of flows (e.g. Mediterranean Sea, flow to detritus: 42%; other EU seas, consumption: 43-48%) driving the system and the cycling indices. This suggested higher levels of community stress induced by intensive fishing activities in the Mediterranean basin. This study constitutes the first attempt to build an historical and current food web model for the whole Mediterranean Sea.