The Neotropics are home to incomparable plant diversity. To evaluate the potential roles of geography and ecology on speciation in Neotropical plants we selected a small, tractable lineage of shrubby angiosperms, Piper subgenus Ottonia. We reconstructed a molecular phylogeny and provided insights into the species divergence times based on fossil calibration of the molecular clock. We support the monophyly of Piper subg. Ottonia and the two main lineages: Amazonian and Atlantic Forest, the latter containing the non-Atlantic species pair P. darienense—P. piscatorum. We also propose the origin of Piper subg. Ottonia in the early Eocene and suggest that the diversification of Piper subg. Ottonia was influenced by geo-historical events such as the Paleocene-Eocene Thermal Maximum (PETM) and the uplift of the Andes in the Miocene, as is the case for other angiosperms. Furthermore, we combined our phylogeny with geographic and environmental data in order to evaluate geographical and ecological contexts for speciation. We indicate that neither climatic/edaphic divergence nor geographic isolation appears to be needed to explain speciation in this lineage.