In this study, the data on calcareous nanoplankton from the Quaternary sediments of the sites drilled by D/Vs Glomar Challenger and Joides Resolution in the Southern Ocean were used. More than 20 areals of different species allowed us to compile a scheme of biogeographic zoning for two time intervals (Early Pleistocene and Late Pleistocene-Holocene). Criteria for identification are elaborated and paleoecological groups, on the basis of which the Polar (Antarctic), Subpolar (Subantarctic), Moderate (Notal), and Subtropical zones were established, are presented. Their changes during the Quaternary show a cooling of the climate in individual regions of the Southern Ocean from the Early to the Late Pleistocene.