Paleogene dinoflagellate cysts were recorded from the Chorrillo Chico and Agua Fresca formations at Punta Prat, southern Chile. Due to the presence of Palaeoperidinium pyrophorum, the Chorrillo Chico Formation is no younger than Late Selandian. By comparison with other basins, a Late Danian to Late Selandian age is proposed for the Chorrillo Chico Formation at Punta Prat. The Paleocene–Eocene boundary is characterized by Apectodinium-dominated assemblages in the mid and high latitudes, the Atlantic coast of Isla Grande de Tierra del Fuego in Argentina, and Chile. The absence of this event at Punta Prat suggests a regional hiatus across the Paleocene–Eocene boundary. An Early to Middle Eocene age is assigned to the lower part of the Agua Fresca Formation by comparison with dinoflagellate cyst assemblages from elsewhere in the Southern Hemisphere.