Forty-seven rock samples from the stratotypes of three upper Paleogene formations – Prussian, Palvé, and Kurshskaya formations – were collected from the biggest amber deposit worldwide (Primorsky quarry, Kaliningrad Oblast SE Baltic coast), and have been palynologically analyzed. The presence of age-diagnostic dinoflagellate cyst species has allowed us to refine and update the previously questionable age of regional lithostratigraphical units. Based on the presence of Rhombodinium perforatum, the ‘Upper Wild Earth’ and ‘Upper Blue Earth’ members of the Prussian Formation correspond to the early Priabonian (Late Eocene) Rhombodinium perforatum Zone. The overlying ‘Upper Quicksand’ and ‘White Wall’ members of the Prussian Formation contain the key-species Thalassiphora reticulata, and are correlated with the latest Priabonian T. reticulata Zone. The overlying Palvé Fm (‘Green Wall’), comprises a dinoflagellate cyst assemblage very close to that recorded from the Prussian Formation, and also corresponds to the T. reticulata Zone, late Priabonian. The lower part of the Kurshskaya Formation – ‘Chocolate clays’ and lower ‘Brown sands’ members, contain an impoverished dinoflagellate cyst assemblages as a result of significant environmental changes. However, the common presence of Areosphaeridium diktyoplokum and Glaphyrocysta semitecta, along with an absence of early Oligocene key-species Wetzeliella gochtii or Chiropteridium galea, and pollen key-species Boehlensipollis hohli or Aglaoreidia cyclops, suggest the lower Kurshskaya Formation can be correlated with the uppermost Eocene, and very close to the Eocene/Oligocene boundary. Based on the revised stratigraphical ages presented here, we suggest an important regional marine transgression occurred during the Priabonian, which allowed the direct marine connection between the NW European Basin and Peri-Tethys via the Polish-Luthuanian Seaway. This was then followed by a regression at the end of Priabonian that culminated in a transition to continental sedimentation in the early Rupelian. A new dinoflagellate cyst species Oligokolpoma balticus sp. nov. is formally described.