Rich and well-preserved assemblages of organic walled dinoflagellate cysts in 50 samples from a 154 m thick and almost complete, Middle Eocene to ?lowermost Oligocene section from the Kysing Research Borehole in eastern Jylland, Denmark are systematically described. One genus Costacysta gen. nov., and twelve species Chiropteridium eocaenicum sp. nov., Costacysta bucina gen. et sp. nov., Distatodinium pilosum sp. nov., Echinidinium? lucidum sp. nov., Hapsocysta kysingensis sp. nov., Horologinella? pentagonalis sp. nov., Operculodinium eisenackii sp. nov., Phthanoperidinium cornutum sp. nov., Selenopemphix septum sp. nov., Svalbardella partimtabulata sp. nov., Thalassiphora gracilis sp. nov. and Thalassiphora microperforata sp. nov. are formally described. The genus Hapsocysta is emended, and is considered to be a senior synonym of Piccoladinium. The gradual change of the dinoflagellate cyst assemblages in this section demonstrates that sedimentation was almost continuous during the time span of ca. 12 Ma. The biostratigraphic resolution based on dinoflagellate cyst events is generally finer than the calcareous nannofossil NP biozonation. A comparison with published dinoflagellate cyst data from the Norwegian–Greenland Sea shows that several important events are mainly synchronous throughout the region, suggesting a general similarity of the water masses. An isolated occurrence of Svalbardella suggests a short cooling event during early Bartonian times. The palynofacies in most of the section is almost purely of pelagic type. A more proximal, mid shelf palynofacies and a distinctive episode of reworking coincide with the Upper Eocene Moesgaard Clay and indicate a brief, but rather large sea level fall during the deposition of this unit. The Eocene/Oligocene boundary is tentatively identified near the base of the Viborg Formation, and approximately coincides with increased reworking of dinoflagellate cysts and a strong increase in bisaccate pollen, indicating more proximal conditions and possibly also a climatic cooling.