Basidiomycota are an ecologically and taxonomically diverse fungal phylum, colonizing all terrestrial ecosystems, with 30,000 described species. By contrast, in marine habitats Basidiomycota are underrepresented when compared to the more abundant Ascomycota. Recently, we investigated the marine mycobiota mainly in the Mediterranean Sea, confirming the scarcity of Basidiomycota. However, a low rank taxonomic identification based on morphological features, proved impossible, since most of the strains remained sterile in axenic culture. Nevertheless, considering the great potential and biotechnological value of Basidiomycota, it would be useful to define their precise taxonomic placement. To this end, 34 marine Basidiomycota isolated from different marine substrates underwent molecular analyses and 123 newly generated sequences were obtained and deposited in GenBank. Sequencing of the Internal Transcribed Spacer (nrITS) regions allowed us to affiliate the 34 strains with six classes, but a lower taxonomic identification was reached with a multi-locus phylogenetic analysis.