The advent of Sanger sequencing represented a scientific break-through that greatly advanced biogeographic studies. However, this technology has several limitations that have hampered more advanced studies in the field. The development of novel techniques which more fully exploit the potential of Massively Parallel Sequencing (MPS) to deliver sequence data at a fraction of the cost of Sanger sequencing promises to revolutionize biogeographic studies. Approaches like Restriction-site Associated DNA sequencing (RADseq) and UltraConserved Element (UCE) sequencing enable the collection of unprecedented amounts of data for multi-locus studies of population genetics and phylogenetics respectively, which in turn can be used for biogeographic analysis. Here we review those and other methods related to MPS, and provide examples of how they can be used in tropical Atlantic biogeography.