Despite warm polar climates and low meridional temperature gradients, a number of different high-latitude plankton assemblages were, to varying extents, dominated by endemic species during most of the Paleogene. To better understand the evolution of Paleogene plankton endemism in the high southern latitudes, we investigate the spatiotemporal distribution of the fossil remains of dinoflagellates, i.e., organic-walled cysts (dinocysts), and their response to changes in regional sea surface temperature (SST). We show that Paleocene and early Eocene (∼65–50 Ma) Southern Ocean dinocyst assemblages were largely cosmopolitan in nature but that a distinct switch from cosmopolitan-dominated to endemic-dominated assemblages (the so-called “transantarctic flora”) occurred around the early-middle Eocene boundary (∼50 Ma). The spatial distribution and relative abundance patterns of this transantarctic flora correspond well with surface water circulation patterns as reconstructed through general circulation model experiments throughout the Eocene. We quantitatively compare dinocyst assemblages with previously published TEX86–based SST reconstructions through the early and middle Eocene from a key locality in the southwest Pacific Ocean, ODP Leg 189 Site 1172 on the East Tasman Plateau. We conclude that the middle Eocene onset of the proliferation of the transantarctic flora is not linearly correlated with regional SST records and that only after the transantarctic flora became fully established later in the middle Eocene, possibly triggered by large-scale changes in surface-ocean nutrient availability, were abundances of endemic dinocysts modulated by regional SST variations.