Synthesis of ecological and evolutionary concepts and tools has led to improved understanding of how diversification, dispersal, community assembly, long-term coexistence and extinction shape patterns of biological diversity. Phylogeography, with its focus on Quaternary interactions within and between populations, can help elucidate the processes acting between the evolutionary time-scales on which species arise and the ecological time-scales on which members of an assemblage interact with each other and their environment. Still, it has yet to be widely incorporated in that synthesis. Here, we highlight three areas where integration of phylogeography with ecological and evolutionary approaches can provide new insights into key questions. First, phylogeography can help clarify the roles of isolation, niche conservatism and environmental stability in generating patterns of alpha- and beta-diversity. Second, phylogeography can help isolate the effects of Quaternary dispersal limitation from other factors driving community assembly and spatial turnover. Third, phylogeography can help identify key processes leading to and resulting from extinction events, including the population dynamics of species range reduction and its effects on the strength and temporal flexibility of networks of species interactions. We conclude with an outlook on the data-gathering protocols necessary for this collaborative, interdisciplinary research agenda.