Palynological data from offshore Costa Rica, allow us to investigate the relationship between dinoflagellate cyst assemblages and changes in regional oceanic primary productivity. From Miocene to Pleistocene, productivity at ODP Site 1039 was influenced by tectonic drift, as Site 1039 approached the continent, from the Equator to its current position at approximately 10 degrees N. In addition, dinoflagellate abundance is modulated by regional productivity events, which modified primary productivity, as also indicated by available data on calcareous nannofossils, diatoms, TOC, and CaCO (sub 3) content. Five palynomorph intervals are defined. The early-late Miocene one, dominated by Batiacasphaera, represents relatively stable, productive oceanic conditions before the closure of the Indonesian and Panama Seaways. The late Miocene decrease in palynomorph recovery is related to the Carbonate Crash Event. The high abundance and diversity of the assemblages at the end of the late Miocene to early Pliocene indicate increased productivity related to the Global Biogenic Bloom, and a change in dominance from Batiacasphaera to Impagidinium to Nematosphaeropsis. The low abundance of the late Pliocene interval is related to El Nino-like conditions, and there is another change related to the disappearance of Batiacasphaera and dominance of Impagidinium, Nematosphaeropsis, and Operculodinium. The abundant Pleistocene assemblages represent increased marine productivity, and a high influx of continental palynomorphs and bissacate pollen, associated with the proximity of the Costa Rica Dome. Pleistocene dinoflagellates are characterized by Spiniferites and Selenopemphix, together with rare Impagidinium and Nematosphaeropsis. Abstract Copyright (2011) Elsevier, B.V.