Cenozoic palaeoceanography of the SE Atlantic and Southern Oceans has been investigated using Late Eocene/Early Oligocene to Quaternary ostracod assemblages from 49 samples of ODP Sites 1087 and 1088. Although the overall abundance of ostracods is relatively low (means of 17 and 49 specimens per sample at Sites 1087 and 1088, respectively) and there is an apparently high level of endemism (ranging from 50% to 80% at Sites 1087 and 1088), three major changes in the faunal assemblages are identified at Site 1087 (denoted A, B and C) and two at Site 1088 (denoted B′ and C′). The assemblage boundaries, detected on the basis of stepwise changes in the abundance, diversity, dominance, endemism, faunal turnover and relative abundance of common taxa, coincide broadly with previously identified, ostracod-based palaeoceanographical ‘events’ discussed by Benson and co-workers over the last two decades. The data do not extend sufficiently far back to record the initiation of Assemblage A, but the faunal change between Assemblages A and B, marked by a decline in abundance, species diversity and faunal turnover, occurs within the Middle Miocene (NN5-6). It coincides with a previously documented palaeoceanographical ‘event’ at 16–14 Ma which, we suggest, may be related to the initiation of North Atlantic Deep Water (NADW) production and/or an expansion of the East Antarctic ice sheet. Assemblage B′ is subdivided into the two Sub-assemblages B′1 and B′2 mainly on the basis of an increase in diversity, a peak in faunal turnover and a drop in the relative abundance of the genus Krithe in early Late Miocene time (NN9, c. 10.5 Ma). The B′1/B′2 Sub-assemblage boundary cannot be related to any previously documented faunal change in deep-sea ostracods. Changes associated with the boundaries between Assemblages B and C, and B′ and C′, which we believe to be synchronous, both include a decrease in diversity and abundance. In addition, two strong turnover peaks occur near the B′/C′ boundary at Site 1088. The B/C and B′/C′ boundaries coincide with a previously documented midPliocene ‘event’ (3.5 Ma) (NN15-16) which may be linked to putative closure of the Straits of Panama and increased production of NADW, the latter in turn leading to increased production of Antarctic Intermediate Water (AAIW) and Antarctic Bottom Water (AABW). Alternatively, fiuctuations in size of the Antarctic ice sheet during possible Pliocene warm periods could indirectly be responsible for the observed midPliocene faunal changes.