Since evolutionary processes, such as dispersal, adaptation and drift, occur in a geographical context, at multiple hierarchical levels, biogeography provides a central and important unifying framework for understanding the patterns of distribution of life on Earth. However, the advent of molecular markers has allowed a clearer evaluation of the relationships between microevolutionary processes and patterns of genetic divergence among populations in geographical space, triggering the rapid development of many research programmes. Here we provide an overview of the interpretation of patterns of genetic diversity in geographical and ecological space, using both implicit and explicit spatial approaches. We discuss the actual or potential interaction of phylogeography, molecular ecology, ecological genetics, geographical genetics, landscape genetics and conservation genetics with biogeography, identifying their respective roles and their ability to deal with ecological and evolutionary processes at different levels of the biological hierarchy. We also discuss how each of these research programmes can improve strategies for biodiversity conservation. A unification of these research programmes is needed to better achieve their goals, and to do this it is important to develop cross-disciplinary communication and collaborations among geneticists, ecologists, biogeographers and spatial statisticians.