This project collects the genomic and transcriptomic data generated for Mesoplodon bidens, common name Sowerby's beaked whale, as part of the European Reference Genome Atlas Pilot Project (https://www.erga-biodiversity.eu/pilot-project). The data under this project are made available subject to the Tree of Life Open Data Release Policy (https://www.darwintreeoflife.org/project-resources/). The assembly is provided by the Wellcome Sanger Institute Tree of Life Programme (https://www.sanger.ac.uk/programme/tree-of-life/) in collaboration with Thomas Lyrholm (Swedish Museum of Natural History), species ambassador for ERGA, and the European Reference Genome Atlas Pilot Project team.