In Colombia, palynology has been widely used as a biostratigraphic tool in oil exploration over the last two decades and, as a result of these efforts, an understanding of the chronostratigraphic range of thousands of palynomorph species is now available. Furthermore, because of their relative resistance to physical and chemical degradation, palynomorphs can often survive several tectonic-erosive cycles, allowing them to be used as unique tracers of long-term sedimentological changes. In this work, we use the palynological record from wells and outcrops in the Llanos foothills and the Llanos basin of Colombia to establish the intensity of Cenozoic reworking and its relationship to the tectonic evolution of the Colombian Andes. Using this approach, we were able to discern several tectonic episodes associated with the uplift of the Eastern Cordillera. We documented three periods of either faster erosion in the hinterland or more widespread areas being eroded in the catchment areas (late Paleocene–early Eocene, early to mid Miocene and Pliocene) and two periods of tectonic quiescence (mid-Eocene and mid–late Miocene). These periods correlate well with the deposition of different elements of the petroleum systems in the Llanos basin of Colombia (seals and reservoirs).