▪ Abstract Understanding the evolutionary processes that generate and sustain diversity in tropical faunas has challenged biologists for over a century and should underpin conservation strategies. Molecular studies of diversity within species and relationships among species, when integrated with more traditional approaches of biogeography and paleoecology, have much to contribute to this challenge. Here we outline the current major hypotheses, develop predictions relevant to integrated molecular approaches, and evaluate the current evidence, focusing on central African, Australian, and South American systems. The available data are sparse relative to the scale of the questions. However, the following conclusions can be drawn: (a) in most cases, the divergence of extant sister taxa predates the Pleistocene; (b) areas with high habitat heterogeneity and recent climatic or geological instability appear to harbor more species of recent origin; (c) there is support for both allopatric and gradient models of diversification and more attention should be given to the role of diversifying selection regardless of geographic context; and (d) conservation strategies should seek to protect heterogeneous landscapes within and adjacent to large rainforest areas, rather than rainforests alone.