This paper presents a sequence-stratigraphic interpretation from the palynological analysis and lithologic data of two outcrop sections on the NE flank of the Upper Magdalena Valley (UMV) basin primarily comprising the Santonian–Lower Maastrichtian interval. Important stratal horizons are identified in the northeastern part of the UMV basin and ages assigned to them. A cyclic pattern of palynomorph distribution was recognized in both sections and tied to the different stages of the stratigraphic chart. Spikes in abundance of spores accompanied by pollen characterize the lowstand systems tracts and are replaced by the occurrence of euryhaline dinoflagellate cysts (ceratioids and/or gymnodinioids) during the subsequent transgressive phase. Maximum flooding surfaces (MFS) are recognized by a sudden increase in open marine palynomorphs (peridinioids and/or gonyaulacoids) and the scarcity of terrestrial representatives. As sea level starts to fall, the gradual decrease in open marine dinoflagellates along with the occurrence of euryhaline dinoflagellate cysts and terrestrial representatives corresponds to highstand systems tracts. The sequence-stratigraphic interpretation from palynological analysis was correlated to the global sea-level curve allowing the identification of the Santonian–Campanian and Campanian–Maastrichtian boundaries. System tracts from supercycles ZC-3, ZC-4 and TA-1 were recognized from the palynological data.