Plankton plays an important role in the functioning of marine ecosystems, for example, through their role as prey. It is therefore important to understand the spatial distribution of assemblages of key taxa. This study aimed to determine the effect of hydrologic and topographic features on two major macrozooplankton groups: euphausiids and amphipods, which are important prey of seabirds and marine mammals. The biogeography of these taxa’s species between the Southern Indian Ocean and the North Indian sector of the Southern Ocean will be assessed by network analyses on species abundances. Our results from the REPCCOAI surveys from 2017 to 2019 between Crozet, Kerguelen and St Paul and New Amsterdam revealed a strong biogeographic separation between the subtropical and subantarctic zones. Species assemblages for each major taxon revealed a distinction between off shelf areas and the neritic zone and between high and low productivity areas, underlining the role of the subantarctic islands and their effect on primary production in the biogeography of the southern plankton. In the subtropical Indian Ocean, no significant major distinction was observed with the network analysis, even if some sites seem to show an influence of the Agulhas Return Current.