Abstract The composition, distribution, abundance, biomass and size structure of mesozooplankton, collected using Bongo nets in the top 300 m layer along a transect between the Antarctic continent and Cape Town, were investigated during the second South African Antarctic Marine Ecosystem Study (SAAMES II) in Jan.–Feb. 1993. Small (<10 mm) and medium (20–50 mm) size groups of zooplankton consistently dominated across the Southern Ocean. The highest zooplankton densities were recorded at the Antarctic Polar Front (APF) and at the Subtropical Convergence (STC). Minor peaks in zooplankton densities were observed in the southern vicinity of the Subantarctic Front (SAF) and APF. Elevated zooplankton stocks were also found within the Marginal Ice Zone (MIZ) and the Polar Frontal Zone. The lowest densities were recorded in the permanently open zone (MIZ–APF) and in the Subantarctic zone (SAF–STC). Copepods were generally important along the entire transect and formed the bulk of zooplankton stock within the MIZ and in the Polar Frontal Zone (APF–SAF), accounting for at least 40–95% of total abundance and biomass. Euphausiids were also a prominent group along the transect. Their contribution was highest (up to 80% of total biomass) between the MIZ and the APF, mainly because of the occurrence of swarms of the Antarctic krill Euphausia superba. Tunicates, Pyrosoma sp. and Salpa fusiformis, were found in great numbers only in the region of the STC and further north, while Salpa thompsoni was abundant at the southern boundary of the APF. Chaetognaths dominated samples numerically and by mass in the Subantarctic Zone. Results obtained from cluster and ordination analyses show that zooplankton community structure was well correlated with the position of various biogeographical zones separated by the main frontal systems of the Southern Ocean. Two major groupings of stations, separated by the SAF, were identified in these analyses. This front separated the Antarctic and the subantarctic/subtropical assemblages, confirming its important role as a biogeographical boundary.