Abstract.Microzooplankton grazing and protozooplankton community structure was investigated in austral summer (Jan./Feb.) and winter (June/July) 1993 in the Atlantic sector of the Southern Ocean during the SAAMES (South African Antarctic Marine Ecosystem Study) Il and III cruises. Grazing was estimated at 22 stations in summer and at 15 stations in winter by employing the sequential dilution technique. Nano‐heterotrophic flagellates (<20 μm) and ciliates (aloricate ciliates and tintinnids) dominated the protozooplankton assemblages along both transects. Densities in winter were, however, nearly an order of magnitude lower than in summer. Microzooplankton grazing removed between 0 and 28% (mean = 13.2%) of the initial phytoplankton stock in summer and, between 24 and 51 % of the initial stock (mean = 37.6%) in winter. The potential primary production removed during summer ranged between 0 and 46% (mean = 22.0%) compared with the winter range of 56–83% (mean = 67.2%). Size selectivity grazing experiments conducted during both studies suggest that microzooplankton preferentially graze on the nano‐ (20–2.0μm) and picophytoplankton (2.0–0.2μm) size fractions. These results have important implications for the efficiency of the carbon pump in the Southern Ocean. During summer when the larger cells dominate phytoplankton biomass, the bulk of the photosynthetically fixed carbon appears to be channelled to the meso‐ and macrozooplankton fractions. This results in a rapid transfer of organic carbon out of the zone of regeneration to the deep ocean via vertical migration and large faecal pellet production. During winter, however, an increase in the contribution of the smaller size fractions to total phytoplankton biomass results in a greater proportion of the photosynthetically fixed carbon being channelled to the microzooplankton fraction. The efficiency of the carbon pump is, therefore, reduced in that the transfer of carbon below the zone of regeneration is reduced as carbon is recycled mostly within the microbial loop in the upp