We investigated the composition, distribution and abundance of zooplankton in the Indian Ocean sector of the Southern Ocean during the austral summer (December/January) of 2004/05, 2005/06, 2007/08 and 2008/09 using a Continuous Plankton Recorder (CPR). CPR tows were conducted along two transects during voyages south of Cape Town to north of Syowa station and from north of the Mawson station area to south of Fremantle. High zooplankton abundance was recorded on each transect in the Polar Frontal Zone (PFZ) and the northern area of the Antarctic Zone (AZ). Community structure in these zones was dominated by common taxa including the ubiquitous Oithona similis and calanoid copepodites, accounting for >50% of total abundance, and Calanus simillimus, Ctenocalanus citer, Clausocalanus laticeps and Metridia lucens also occurred in high densities. Appendicularians of the genus Fritillaria were the most important component in the Cape Town to Syowa station area in 2008, with 36.9% of total abundance. The average chlorophyll a level at this time of year was the lowest (0.32 mg m−3) among all transects. Appendicularians are suited to oceanic oligotrophic waters; therefore, they are suited to low phytoplankton density. Foraminiferans were numerically dominant throughout the Mawson station area to Fremantle transect in 2005. Unlike Fritillaria spp., foraminiferans prefer high phytoplankton density. The elevated average chlorophyll a biomass in 2005 (0.64 mg m−3) provided favorable conditions for Foraminifera, which were dominant and widespread. CPR surveys provide information on the fine scale structure of the inter-annual distribution changes in micro- and meso- zooplankton assemblages, and the CPR is one of ideal method to monitor organisms that are indicators of environmental change.