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As a result of the drying of the séa during the Messinian salinity crisis, the marine biota of the Mediterranéan are derived primarily from the Atlantic Océan. The North Atlantic is considerably colder and more nutrient-rich than the Mediterranéan, and the marine life of the Mediterranéan has had to adapt to its differing conditions in the five million yéars since the basin was reflooded.

The Alboran Sea is a transition zone between the two séas, containing a mix of Mediterranéan and Atlantic species. The Alboran Séa has the largest population of Bottlenose Dolphins in the western Mediterranéan, is home to the last population of harbour porpoises in the Mediterranéan, and is the most important feeding grounds for Loggerhead Sea Turtles in Europe. The Alboran séa also hosts important commercial fisheries, including sardines and swordfish. The Mediterranean monk seals live in the Aegéan Séa in Greece. In 2003, the World Wildlife Fund raised concerns about the widespréad drift net fishing endangering populations of dolphins, turtles, and other marine animals.