Abundance data (individuals.m-3) of large microzooplankton assemblages collected during two “Acoustics along the Brazilian coast” surveys (ABRACOS 1 and ABRACOS 2) performed along the northeast Brazilian continental shelf and slope between 5 and 9° S and around oceanic seamounts and islands from Fernando de Noronha ridge, including the Fernando de Noronha Archipelago itself and the Rocas Atoll. The surveys were carried out on board the French oceanographic vessel R/V Antea in austral spring (September–October 2015) and autumn (April–May 2017). Planktonic cnidarians were sorted from zooplankton samples collected at 34 and 45 stations in spring and autumn, respectively. Samples were collected through oblique hauls, with a Bongo net with a 64 µm mesh size and 0.3 m mouth opening. The water column was sampled from near the bottom to the surface over the continental shelf and from 200 m to the surface in the offshore. The net was towed at approximately 2 knots, at various times of day and night.