This dataset contains values of numerical abundance and biomass of mesopelagic fish collected during the cruise FLUXES I from 12th of July to the 9th of August 2017, across the Cape Verde Frontal Zone (CVFZ), located in the Central Eastern Atlantic Ocean. Fish were sampled using multi-sampler for collecting samples from 7 different depth layers, and the Multiple Opening/Closing Net and Environmental Sensing System (MOCNESS-1 m²) zooplankton net (Wiebe et al., 1985, doi:10.1007/BF00397811) with a 0.2 mm mesh size and with several nets for collecting samples from 8 different depth layers. Collected specimens MOCNESS-1 samples were preserved in 5% buffered formalin, and specimens were sorted out later. The collected specimens were identified to the lowest possible taxonomic level and measured in the laboratory (Standard lengths, SL; 0.1 mm). The wet weight (WW, 0.1 mg) was measured at the land-based laboratory with an electrical balance (COBOS, AUW 220D ± 0.01 g), and eviscerated dry weight (eDW, 0.1 mg) were obtained from SL using relationships between SL and WW or eDW obtained from the literature (López-Pérez et al., 2020, doi:10.1111/jfb.14307). Abundance and biomass are given by layer.