This is a unified and revised marine fossil record of the Mediterranean covering the Tortonian stage, the pre-evaporitic Messinian and the Zanclean stage and encompassing 23032 occurrences of calcareous nannoplankton, dinoflagellates, foraminifera, corals, ostracods, bryozoans, echinoids, mollusks, fishes, and marine mammals. It consists of four files in .csv format: 1) 'MessinianDB' contains the fossil occurrences; 2) 'coord' has the list of fossiliferous localities with their coordinates and the groups of organisms reported from each one; 3) 'DBrefs' contains the full citations of the references in the database; 4) 'corals' contains the list of coral genera in the database, indicating whether or not they include zooxanthellate (z-corals) or azooxanthellate (az-corals) species, or both. In the latter case, we further indicate if the species found in the database should be considered z- or az-corals, based on the accompanying fauna.