The evolution of the tropical lowland forests in northern South America is poorly understood, yet new insights into past composition and changes through time can be obtained from the rich and diverse fossil pollen record. Here we present a revision of two diagnostic Malvaceae taxa from the Cenozoic record of northern South America and we relate their evolutionary history to recently updated geological models. In our study we review the pollen morphology and botanical affinity of Rhoipites guianensis and Malvacipolloides maristellae, and integrate these data into a phylogenetic framework. We also produce distribution maps for both fossil and extant taxa, infer the phylogeny and historical biogeography of the lineages to which they belong, and identify their ecological associates and environmental settings. The closest extant relatives of Rhoipites guianensis (Grewioideae) are Vasivaea and Trichospermum, which are taxa of South American origin. During the late Eocene to early Miocene Rhoipites guianensis was widely distributed in the lowland floodplain environments of northern South America. The closest living relatives of Malvacipolloides maristellae (Malvoideae) are members of Abutilinae (e.g., Abutilon, Bakeridesia, Callianthe and Herissantia), which have their origin in the northern hemisphere. This taxon makes its first appearance in the fossil record of northern South America during the early Miocene, and is typically found in fresh water floodplain and lacustrine environments. Our study suggests that both taxa migrated across the Central American Seaway in the early Miocene (around 18 Ma), and virtually disappeared from the fossil record in northern South America during the middle Miocene, coinciding with Andean uplift. However, their descendants expanded and -in the case of the Abutilinae—diversified in the Andes. We conclude that the biogeographic history of these Malvaceae is influenced by Andean uplift and the incipient bridging of the Americas. Thereafter, climate change and diversification of the Andean landscape enabled their descendants to move upslope and into the Andes.