The Amazon drainage basin (Amazonia) contains the largest continuous area of tropical rainforest in the world and is the most species-rich terrestrial ecosystem on Earth. In biogeographical terms, the Amazon rainforest is still somewhat of a mystery, beset by data shortfalls in many taxonomic groups, lacking systematic surveys and faced with the challenge of collecting and collating data over a vast area. Nevertheless, considerable progress has been made over the last 20 years, leading to new insights from diverse fields of study. One of the most exciting developments has been the creation of large international research networks which are collating and synthesizing information from widely scattered permanent botanical plots. Data from these networks and other studies are providing valuable new insights on contemporary biodiversity patterns and processes in Amazonia. Here we review the major findings of these networks and discuss the factors that correlate with and may explain the spatial distribution of Amazonian tree species and the factors that may underpin the emergent patterns of functional traits and diversity across the Amazon Basin.