Phylogenetic and phylogeographic approaches have become widespread in evolutionary biology, ecology, and biogeography. However, analyses that incorporate inferences from historical biogeography (e.g. timing of colonization of a region) may be essential to answer the most important large-scale questions in these fields, but they remain infrequently used. I focus on two examples here. First, I argue that understanding the origins of biodiversity hotspots (and other high-diversity regions) requires comparing the timing of biogeographic colonization and diversification rates among regions. In contrast, phylogeographic studies (analyses within species within a region) may themselves say little about why a region is diverse relative to others. Second, incorporating historical biogeograpy can help address the processes that determine community species richness and structure, such as dispersal, in-situ trait evolution, and in-situ speciation. In contrast, the widespread “community phylogenetics” approach (focusing on relatedness of species in communities) may have limited ability to explain community richness and structure.