The occurrence of cultivable fungi was investigated along the water column (25-2500 m depth) of four off-shore stations in the Mediterranean basin. An unexpected high abundance of fungi, accompanied by a scarce biodiversity, was observed up to 2500 m depth. The black yeast Hortaea werneckii, known to be one of the most salt tolerant eukaryotic organisms, was isolated for the first time from the Mediterranean Sea, and it was the dominant fungus present in seawater in almost all stations and depths, suggesting its ubiquitous distribution. Isolation of cultivable strains allowed their phylogenetic and taxonomic characterization, and demonstrated that almost all the retrieved fungal species should be considered of terrestrial origin, but well adapted to survive and reproduce at temperature and salinity conditions of the Mediterranean seawater.