This file contains data on number of mesopelagic fish collected during the CSIC-SUMMER survey carried out in October 2020 in five zones around the Iberian Peninsula: Balears and Alboran in the western Mediterranean, and Cadiz, Lisboa and Galicia. The scientific midwater trawl Mesopelagos fitted with a Multisampler placed at the end of the net was used to collect specimens at seven layers of the water column. The depth of the net was controlled by a SCANMAR system. In the five zones, hauls were carried out day and night to study vertical migration patterns of mesopelagic fish. A total of 24 deployments were made (between 0 and 700 m), of which 14 discriminated water layers. Additionally, to more accurately sample the epipelagic layers 7 night hauls were restricted to the first 210 m of the water column. Fish were identified and counted on board, or frozen for later processes in the laboratory. These data were obtained within the European Union Project 'Sustainable Management of Mesopelagic Resources' (SUMMER, Grant Agreement 817806) as funded by the Horizon 2020 Research and Innovation Programme.