In the framework of the "Developing Optimal and Open Research Support for the Black Sea (DOORS)" project (Horizon 2020 Grant agreement ID: 101000518), sampling was conducted in three locations in the Black Sea. Seawater samples were collected and were later subjected to shotgun metagenomics sequencing, as well as metabarcoding sequencing for 18S rRNA and COI. All procedures follow the EMO BON Handbook.