Fatty acid (FA) composition has increasingly been used to estimate the dietary preference of marine organisms. Specific fatty acids and fatty acid ratios serve as trophic markers (FATM) and have the potential to provide insights on the long-term dietary preference of organisms. FATM have been applied for this purpose on various zooplankton, fish and up to whales. We aim to build up a database of new and published data on fatty acid content of mesopelagic fish and their predators from the central and Northeast Atlantic, and the Mediterranean Sea, to use in FATM food web studies, investigating the importance of mesopelagic organisms as predators and prey in the marine ecosystem. Here we compiled FA content (i.e., the proportion of each FA measured in sampled tissues or in the whole body of organisms in relation to total FAs analysed) of 36 fish species or genera, 15 seabirds, five marine mammals, two cephalopods, one turtle, one jelly fish, and one shark. For each record, we included all FAs with values above 0.1% of total FAs and report the percentage values as provided in the original data source. Each data record is associated with information on the sampling location, geographic coordinates, month and year of sample collection, method of sample collection, taxonomic ranks (phylum, class, order, family), number and size (or size range) of sampled organisms, as well as the reference and DOI of the original data source, for further details on the samples analysed and/or the analytical techniques used.