The combustion of fossil fuels and the resultant impacts on climate may now represent one of the largest environmental threats. In the Mediterranean Sea, changes in bio-chemical and physical seawater properties resulting from global warming are likely to alter marine biodiversity and productivity, trigger trophic web mismatches and encourage diseases, toxic algal bloom and propagation of thermophilic species. This review highlights the current and potential threats of climate change to the Mediterranean marine ecosystems, including cetaceans, and stresses the emergent necessity for more integrated regulations and policies for the protection of marine biodiversity. For instance, in the Mediterranean Sea, the distribution and abundance of the small euphausid species Meganyctiphanes norvegica is correlated with specific hydrobiological parameters including seawater temperature, salinity and current patterns. Situated at the northern limit of its ecological tolerance, this species, which constitutes the only known food supply of the fin whales (Balaenoptera physalus) in this region, might be affected by climate change-induced alteration of ocean circulation.