A new model was developed for the paleogeographic distribution of dinoflagellate cysts across the Cretaceous/Paleogene (K/Pg) boundary. Four sections in the Eastern Alps were studied. The Knappengraben and Gamsbach sections are located in the Gosau Basin of Gams, Austria. They are continuous across the boundary and represent a bathyal environment. The Waidach section north of Salzburg (Austria) contains neritic deposits of the Helvetic unit but shows a hiatus at the boundary. The Goppling section between Teisendorf and Oberteisendorf (Bavaria, Germany) belongs to a turbidite-rich, deep-water system (Ultrahelvetic unit), and is considered to be continuous across the boundary.The occurrence and distribution of dinoflagellate cysts in these sections suggests that Trabeculidinium, Adnatosphaeridium, Spiniferites, Pterodinium, Impagidinium, Achomosphaera and Codoniella are restricted to bathyal environments, whereas Areoligera, Manumiella and Trithyrodinium are restricted to the neritic environment. The abundance of Manumiella and Trithyrodinium indicate a high nutrient supply. Hystrichosphaeridium -dominated assemblages have been recorded in both neritic and bathyal environments. Two Manumiella spikes were recorded only at Waidach and interpreted to reflect slight coolings of oceanic surface waters. In the Danian, acme of Spongodinium delitiense are recorded ~1 m above the K/Pg boundary in the neritic and bathyal environments. These acmes could reflect a slight cooling of surface waters in the earliest Danian.The palynofacies analysis in the Gams Basin reveals a high abundance of amorphous organic matter in the Maastrichtian, and black phytoclasts in the Danian, which indicates intensified terrigenous run-off in the Danian with higher sea-floor oxygenation. In the Waidach section, palynomorphs are much more abundant, indicating a shelf to basin transitional area with dysoxic-anoxic conditions at the sea-floor.