Hortaea werneckii belongs to the so-called black yeast, a polyphyletic group of pleomorphic and melanised fungi that present in many cases a polyextremotolerant life style. The aim of this study was to deep inside the genomic characteristics of two further H. werneckii strains isolated from Mediterranean Sea at 3,400 and 2,200 m depth respectively. A comparative genome analysis with other 12 published H. werneckii genomes, from different environmental sources, was also carried out to investigate the evolutionary history and the possible marine origin of the strains from the deep sea.