The Mediterranean Sea is a marine biodiversity hot spot. Here we combined an extensive literature analysis with expert opinions to update publicly available estimates of major taxa in this marine ecosystem and to revise and update several species lists. We also assessed overall spatial and temporal patterns of species diversity and identified major changes and threats. Our results listed approximately 17,000 marine species occurring in the Mediterranean Sea. However, our estimates of marine diversity are still incomplete as yet—undescribed species will be added in the future. Diversity for microbes is substantially underestimated, and the deep-sea areas and portions of the southern and eastern region are still poorly known. In addition, the invasion of alien species is a crucial factor that will continue to change the biodiversity of the Mediterranean, mainly in its eastern basin that can spread rapidly northwards and westwards due to the warming of the Mediterranean Sea. Spatial patterns showed a general decrease in biodiversity from northwestern to southeastern regions following a gradient of production, with some exceptions and caution due to gaps in our knowledge of the biota along the southern and eastern rims. Biodiversity was also generally higher in coastal areas and continental shelves, and decreases with depth. Temporal trends indicated that overexploitation and habitat loss have been the main human drivers of historical changes in biodiversity. At present, habitat loss and degradation, followed by fishing impacts, pollution, climate change, eutrophication, and the establishment of alien species are the most important threats and affect the greatest number of taxonomic groups. All these impacts are expected to grow in importance in the future, especially climate change and habitat degradation. The spatial identification of hot spots highlighted the ecological importance of most of the western Mediterranean shelves (and in particular, the Strait of Gibraltar and the adjacent Alboran Sea), western African coast, the Adriatic, and the Aegean Sea, which show high concentrations of endangered, threatened, or vulnerable species. The Levantine Basin, severely impacted by the invasion of species, is endangered as well ; 35 pages, 14 figures, 3 tables ; The authors gratefully acknowledge the support given by the European Census of Marine Life, the Total Foundation and the Alfred P. Sloan Foundation. MC was supported financially by the European Commission Marie Curie Postdoctoral Fellowship through the International Outgoing Fellowships (Call FP7-PEOPLE-2007-4-1-IOF) for the ECOFUN project and by Dalhousie University (Halifax, Canada). EB acknowledges financial support from GRACCIE project C5D2007-00067 funded by the Spanish Ministry of Science and Innovation. BG thanks the support of SESAME funded by the European Commission's Sixth Framework Program on Sustainable Development, Global Change and Ecosystems. JISS acknowledges ECOLIFE (CGL2008-05407-C03-03) funds of the Ministry of Science and Innovation of Spain. The present paper is a contribution of JG, DM and XT to the projects 2009SRG665 and 2009SGR484 of the “Generalitat de Catalunya”, and of DM and XT to project CTM2007-66635 funded by the Ministry of Science and Innovation of Spain. Research by C. N. Bianchi on Mediterranean Sea biodiversity is partly supported by the project “The impacts of biological invasions and climate change on the biodiversity of the Mediterranean Sea” (Italy-Israel co-operation) funded by the Italian Ministry of the Environment