The rapid growth of techniques employed in the generation and analysis of DNA variation has led to significant advances throughout the life sciences. Herein, we explore the impacts of this molecular revolution on the science of biogeography and how it has enhanced or altered long-standing biogeographic hypotheses in this revitalized discipline. We examine the recent development of molecular biogeography and address issues dealing with data generation and interpretation and review newer analytical techniques that have been developed to handle the explosion of available data. We explore several important issues, including analyses of molecular time estimates and phylogenetic, phylogeographic and population genetic approaches to reconstructing the evolutionary histories of taxa and whole biotas. Specialized topics of growing importance include advances in the use of ancient DNA and the importance of incorporating biogeographic theory with DNA barcodes, used to catalog the diversity of life. Finally, we investigate some of the newest and most exciting techniques of generating, analyzing and visualizing genetic data that will shape the future of molecular biogeography.