Dinoflagellate cyst assemblages recovered from the La Meseta Formation cropping out in Seymour Island, Antarctic Peninsula, are studied herein and their distribution is compared with the biostratigraphic scheme available for the Palaeogene of the Southern Ocean and other high-latitude regions. In this way, the La Meseta Formation is dated as middle Lutetian to Priabonian (46.2–36 Ma), which differs from the age provided by other fossils, isotopes and also with the magnetostratigraphic scheme recently performed for the unit. The dinoflagellate cyst data support the proposal of ocean circulation patterns on the South American Shelf prior to the opening of Drake Passage. Assemblages from the La Meseta Formation contain Antarctic-endemic taxa which are also dominant in several circum-Antarctic sites, located south of 45° S. Their distribution reflects an ocean-circulation scheme with wide clockwise gyres surrounding Antarctica that were disrupted as a consequence of the deepening and definitive apertures of the Tasmanian Gateway and Drake Passage towards the Eocene/Oligocene transition. The palaeoenvironmental inference based on the S/D ratio (sporomorphs versus dinoflagellate cysts) and the P/G ratio (peridinioid versus gonyaulacoid dinoflagellate cysts) suggests an overall trend through the section from marine-dominated assemblages with poorly productive waters in the lower part of the section to more terrestrially dominated assemblages with increasing productivity in the upper part of the unit, reflecting a shallowing trend to the top.