Oceanic food webs are organized in a continuum from microbial to metazoan linked by trophic interactions. Assessment of the position of organisms in the food web, i.e., their Trophic Level (TL) can be made by from direct analyses of stomach contents or indirectly using tracers like stable isotopes. The present file gives TL for marine organism derived from isotopic data (δ15N) presented in Olivar et al. (submitted to PANGAEA). This file follows a previous data file on TL of mesopelagic organism by Silva et al. (2022) and keeps the same layout. We present estimates of Trophic Levels from 770 samples encompassing 32 species of mesopelagic fish, 7 of crustacean decapods, and 17 species of cetaceans. Fish and crustacean samples come from the temperate Atlantic (Azores, Bay of Biscay, western Iberian Peninsula), and from the western Mediterranean. The baseline to calculate TL for the western Iberian Peninsula and western Mediterranean organisms were the isotopic data of herbivorous copepods obtained concurrently, while for the Bay of Biscay values of the euphausiid Meganyctiphanes norvegica were used. All the cetaceans (order Cetartiodactyla) come from the Azores or the Bay of Biscay. Western Iberian Peninsula and western Mediterranean mesopelagic fish diets from stomach content analyses of the same specimens included in this table are given in Bernal et al. (2023). 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, type of analyses and estimation method, 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.