The present dataset contains coccolithophores abundances (coccospheres/L). The samples were collected between Barcelona and the Ebro Delta (Western Mediterranean), during the MERS-BLUEISLAND cruise in November 2019, with rosette Niskin bottles investigating the photic zone (0-200 m). Quantitative analyses were performed using a polarized light microscope at 1000× magnification. Abundances were determined by counting at least 300 coccospheres per sample when possible. Coccosphere density and species relative abundances were calculated using the following formula: CD = (A × N)/(a × V) where A is the filtration area (mm2), N is the total number of coccospheres, a is the scanned area (mm2) and V is the volume of the filtered water (L). The Upper Photic Zone (UPZ) group includes Rhabdosphaera clavigera, Syracosphaera pulchra, Coronosphaera mediterranea, Umbellosphaera tenuis, Umbellosphaera spp., Discosphaera tubifera, Umbilicosphaera sibogae, Syracosphaera anthos, while Florisphaera profunda and Gladiolithus flabellatus were grouped as Lower Photic Zone (LPZ) taxa. The diversity of the total assemblage was estimated according to Harper (1999, doi:10.1017/S0016756800334410).