This dataset contains values mesozooplankton abundance groups 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). Mesozooplankton 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 with the exception of Protozoa due to the mesh size used was not suitable to retrieve a representative sample (Boltovskoy, 1981). Most abundant mesozooplankton groups were studied and identified until dominant groups. All data were standardized to number of individuals (#/m³) by layer.