The late Paleocene–early Eocene interval was characterized by a long period of global warming that culminated with the highest temperatures of the Tertiary. This interval was also associated with plant extinctions and a subsequent increase in plant diversity in temperate latitudes. However, tropical regions remain largely unknown. We compare the microfloral diversity of the late Paleocene with the late early to middle Eocene in flood plain, coastal plain, and estuarine facies of a section in the Colombian eastern Andes. Several techniques such as range-through method, rarefaction, bootstrap, detrended correspondence analysis, and Simpson index were used to assess the significance of the diversity pattern observed throughout the section. The microfloral record indicates a distinct, diverse Paleocene flora declining toward the end of the Paleocene, being replaced by a different and much more diverse Eocene flora. It is uncertain, however, how these floral changes correlate with the latest Paleocene thermal maximum and Eocene thermal maximum events.