The mesozooplankton samples were collected in the framework of PN19200102 in 15 - 24 September 2020, from 22 stations (29 samples) located along 7 transects (Sulina - SU; Portita - PO; Sfantu Gheorghe - SG; Tuzla - TZ ; Mangalia - MA; Midia - MID; Constanta - CT) crossing the Romanian Black Sea shelf within 15.5 - 149 m bottom depths. The dataset contains qualitative and quantitative data of mesozooplankton taxa collected with a Juday net of 36 cm diameter opening and 150 µm mesh size towed from bottom to certain depth intervals (surface, thermocline, under thermocline) onboard R/V Mare Nigrum. The samples were preserved in 10% formalin onboard and subsequently processed in the NIRD GeoEcoMar laboratory by Mihaela Mureșan, according to Alexandrov et al, 2014. Taxonomic identification was performed to the lowest possible level, individual and total abundances (ind.m-3) and wet biomasses (mg.m-3) were calculated according to Petipa et al., 1957, Alexandrov et al., 2014.