The origin of the great biodiversity observed in tropical South America has spurred debate since the foundational work of Darwin (1859), Agassiz and Agassiz (1868), and Wallace (1878), yet remains one of the great problems of modern science. Wallace (1878) proposed that low extinction rates, resulting from a relatively stable and equitable tropical climate throughout the Cenozoic (the last 65 Ma), enabled the progressive accumulation of species over time, a hypothesis that has been termed the “museum” model. In contrast, the “cradle” model (Stebbins, 1974) posits that most tropical diversity arose from episodic pulses of speciation associated with climatic and geological drivers (Richardson et al., 2001). Resolving these and other conflicting interpretations of the rates and drivers of tropical biodiversity can only be achieved by recovering Cenozoic records of plant composition and diversity in the Amazon region itself and placing these biotic data into a well resolved geologic (surface uplift or subsidence), climatic, phylogenetic, and biogeographic framework.