This dataset contains values of copepods abundance collected during the MAFIA cruise from 31st of March to the 29th of April 2015, from Salvador de Bahía (Brazil) to the Canary Islands (Spain). Species of copepods were sampled using the Multiple Opening/Closing Net and Environmental Sensing System (MOCNESS-1 m²) zooplankton net with a 0.2 mm mesh size and with several nets for collecting samples from 8 different depth layers (0–100 m, separated in two layers depending on the physical-biological scenario, 100–200, 200–300, 300–400, 400–500, 500–600, and 600–800 m depth layers). Collected specimens MOCNESS-1 samples were preserved in 5% buffered formalin, and specimens were sorted out later. All individuals were counted and the dominant species of copepods and cladocerans were identified, whenever possible. All data were standardized to number of individuals (#/m³) by layer.