The organic-walled, hypnozygotic cysts of dinoflagellates (“dinocysts”) provide a rich, albeit incomplete, history of this eukaryotic plankton group in ancient sediments. Building on pioneering studies of the late 1970s and 1980s, recent ocean drilling and more detailed, integrated studies of surface sections have provided a wealth of dino-cyst data spanning the entire Paleogene. Based on multidisciplinary approaches, these studies have been instrumental in refining existing and furnishing new concepts of Paleogene paleoenvironmental and paleoclimatic reconstructions by means of dinocysts. Since dinocysts typically exhibit high abundances in neritic settings, the dinoeyst-based environmental and paleoclimatic information is complementary to that derived from typically more offshore groups such as planktonic foraminifera, coccolithophorids, diatoms, and radiolaria. While in a recent paper we gave a broad overview of case studies from around the globe (Sluijs et al. 2005), here we focus on a summary of these analyses and present a synopsis of applied paleoecological concepts in Paleogene (65–24 ma) dinocyst studies. Representing Earth’s greenhouse-icehouse transition, this episode holds the key to the understanding of extreme transient climatic change. The present paper offers guidelines for the application of dinocyst palaeoecology to the reconstruction of Paleogene sea-surface productivity, temperature, salinity, stratification, and paleo-oxygenation as well as their application in sequence stratigraphy, oceanic circulation and general watermass reconstructions.