Phylogenetic and phylogeographic approaches have become widespread in evolutionary biol‐ ogy, 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 (e.g., 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 rich‐ ness and structure. biodiversity hotspot, biogeography, community ecology, community phylogenetics, phylogeny, phylogeography, species richness