The last four decades have seen an increasing integration of phylogenetics and biogeography. However, a dearth of phylogenetic studies has precluded such biogeographic analyses in South Asia until recently. Noting the increase in phylogenetic research and interest in phylogenetic biogeography in the region, we outline an integrative framework for studying taxon distribution patterns. While doing so, we pay particular attention to challenges posed by the complex geological and ecological history of the region, and the differences in distribution across taxonomic groups. We outline and compare three widely used phylogenetic biogeographic approaches: topology-based methods (TBMs), pattern-based methods (PBMs) and event-based methods (EBMs). TBMs lack a quantitative framework and utilize only part of the available phylogenetic information. Hence, they are mainly suited for preliminary enquiries. Both PBMs and EBMs have a quantitative framework, but we consider the latter to be particularly suited to the South Asian context since they consider multiple biogeographic processes explicitly, and can accommodate a reticulated history of areas. As an illustration, we present a biogeographic analysis of endemic Sri Lankan agamid lizards. The results provide insights into the relative importance of multiple processes and specific zones in the radiation of two speciose lizard clades.