The global importance of mesopelagic fish is increasingly recognised, but they remain relatively poorly studied. This is particularly true in the Southern Ocean, where mesopelagic fishes are both key predators and prey, but where the remote environment makes sampling challenging. Despite this, multiple national Antarctic research programs have undertaken regional sampling of mesopelagic fish over several decades. However, data are dispersed, and sampling methodologies often differ precluding comparisons and limiting synthetic analyses. We identified potential data holders by compiling a metadata catalogue of existing survey data for Southern Ocean mesopelagic fishes. Data holders contributed 17,491 occurrence and 11,190 abundance records from 4780 net hauls from 72 different research cruises. Data span across 37 years from 1991 to 2019 and include trait-based information (length, weight, maturity). The final dataset underwent quality control processes and detailed metadata was provided for each sampling event. This dataset can be accessed through the Antarctic Biodiversity Portal. Myctobase will enhance research capacity by providing the broadscale baseline data necessary for observing and modelling mesopelagic fishes. The paper which this dataset refers to is available at https://doi.org/10.1038/s41597-022-01496-y. The original dataset as submitted for the paper is also available on Zenodo at https://doi.org/10.5281/zenodo.6131579. This dataset is published by SCAR-AntOBIS under the license CC-BY 4.0. We would appreciate it if you could follow the guidelines from the SCAR and IPY Data Policies (https://www.scar.org/excom-meetings/xxxi-scar-delegates-2010-buenos-aires-argentina/4563-scar-xxxi-ip04b-scar-data-policy/file/) when using the data. If you have any questions regarding this dataset, please do not hesitate to contact us via the contact information provided in the metadata or via data-biodiversity-aq@naturalsciences.be. Issues with dataset can be reported at https://github.com/biodiversity-aq/data-publication/ This dataset is part of the Belgian contribution to the EU-Lifewatch project funded by the Belgian Science Policy Office (BELSPO, contract n°FR/36/AN1/AntaBIS) .