Chloranthaceae represent one of the oldest angiosperm lineages. Hedyosmum, with 45 species, is the only Neotropical genus in the family. The first appearance of Hedyosmum-like pollen was in the Early Cretaceous (∼112 Ma). The next unequivocal record of Hedyosmum-like pollen (Clavainaperturites microclavatus) occurred in the early Miocene. The main objective of this study was to determine the relationship between the fossil C. microclavatus and extant representatives of Hedyosmum. Pollen was examined using light, scanning and transmission electron microscopy. Based on a phylogenetic analysis of pollen traits of Chloranthaceae, we concluded that C. microclavatus is related to Hedyosmum. The abundant Neogene fossil evidence of C. microclavatus from South America showed that the ancestor of extant Hedyosmum migrated to tropical South America during the early Miocene and occupied initially lowlands. A comparison of the C. microclavatus fossil record from both Panama and Colombia/Venezuela suggests that the first Neotropical migration of Hedyosmum was from South America to Central America. The abundant Plio-Pleistocene C. microclavatus from Andean regions supports the hypothesis of a recent radiation of the genus as a consequence of the uplift of the tropical Andes. The biogeographic history of Hedyosmum provides an example of recent enrichment of the Neotropical flora.