The paper presents a new study of the Paleogene dinoflagellate cysts from a borehole in central Western Siberia. The presence of stratigraphic markers from the European zonations permitted recognition of six dinoflagellate zones in this section: the Cerodinium speciosum, Apectodinium hyperacanthum and Apectodinium augustum zones in the Paleocene interval; and the Dracodinium varielongitudum, Charlesdowniea coleotrhypta and Charlesdowniea clathrata angulosa zones in the Eocene section. This sequence permits precise age assignment of the Siberian lithological formations, as well as interpretation of the presence of stratigraphic gaps in the marine Siberian Paleogene section. The Late Eocene–Oligocene boundary is characterized by the successive disappearance of the Siberian marine basin and by a significant floristic change.