Isotopic data are valuable to investigate species interactions and food web structure. This file compiles δ13C and δ15N values of various marine taxa; most of data correspond to mesopelagic fish, but mesopelagic cephalopods, decapods and zooplankton, and cetaceans are also represented. This dataset follows a previous data file presented in Silva et al. (2022b) (https://doi.pangaea.de/10.1594/PANGAEA.945917) and maintains the same layout. A total of 1045 records are included, of which 612 correspond to mesopelagic fish (55 species), 18 to non-mesopelagic fish (1 species), 168 to decapods (7 species), 68 to marine mammals (12 species), 5 to Cephalopoda (2 species) and 174 to zooplankton (14 taxa). Data are available for the subarctic and temperate Atlantic, the northeast Atlantic (off the Iberian Peninsula, Azores, and Bay of Biscay), and the Western Mediterranean. Samples come from years 2002 to 2021, and expand to all seasons. The table contains data on bulk stable isotope ratios of carbon (δ13C) and nitrogen (δ15N), and the total organic carbon to nitrogen ratio (C/N) measured in sample tissues or in the whole body of organisms are presented in this file. To eliminate the effect of lipids on δ13C values, lipids were extracted from samples before analysis (column "δ13C_LE (delipized)", or in other cases a mathematical correction was applied a posteriori (column "δ13C_Lipid Corrected"). For each data record, it is provided 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.