The values of natural abundance of stable isotopes were measured in 13 micronekton fish species sampled during the BATHYPELAGIC cruise (North Atlantic, June 2018). This dataset contains the values obtained for carbon and nitrogen in bulk tissues, and nitrogen values in amino acids. Length and biomass data for each individual analyzed are also provided. Fishes were collected using a ''Mesopelagos” net (5x7 m mouth opening, 58 m total lenght) equipped with graded-mesh netting (starting with 30 mm and ending with 4 mm) and a multi-sampler for collecting samples from 5 different depth layers (Olivar et al., 2017). Individual fish were eviscerated, freeze-dried and weighted. Aliquots of muscular tissue (or whole individuals for species of small size) were analyzed in an elemental analyzer (bulk tissues, Olivar et al., 2019) or a gas chromatograph (derivatized amino acids, Mompeán et al., 2016) coupled to isotope-ratio mass spectrometers. Carbon analyses were made before and after removal of lipids with a mixture of trichloromethane:methanol:water. This research was funded by projects BATHYPELAGIC (CTM2016-78853-R) from the Plan Estatal de I+D+I (Spain), SUMMER (Grant Agreement 817806) and TRIATLAS (Grant Agreement 817578), from the European Union (Horizon 2020 Research and Innovation Programme), and Grant Number IN607A2018/2 from the Axencia Galega de Innovación (GAIN, Xunta de Galicia, Spain).