Aim The aim of this review is to contribute to our understanding of the origination of the Sundaic and Indochinese biotas in Southeast Asia. Numerous unsolved problems surround the origination of the differences between these biotas and the determinants of the breadth and current position of the transition between them.Location Literature reviews show that phytogeographical and zoogeographical transitions between the Sundaic and Indochinese subregions lie on the Thai-Malay peninsula just north of the Isthmus of Kra. A second, more widely recognized botanical transition lies 500 km further south at the Kangar-Pattani line near the Thai-Malay border.Results The phytogeographical transition involves 575 genera of plants, and a change from wet seasonal evergreen dipterocarp rain forest to moist mixed deciduous forest. The zoogeographical transition is best characterized for forest birds, and more than half the species present in this region have species boundaries north of the Isthmus of Kra, at 11-13°N latitude. Although the phytogeographical transition is climate-related today, and the avifaunal transition is viewed as being associated with the vegetation change, there is no obvious present day geological, physiographical or environmental feature to account for the origination of the provincial biotas. Similarly, known Neogene palaeoenvironmental changes on the tectonically stable peninsula, including those associated with periods of lower sea levels and the emergence of Sundaland, fail to account for either the origination of the provincial differences or the current position of the transition.Main conclusions Contrary to earlier palaeogeographical reconstructions, it is suggested that Neogene marine transgressions flooded the peninsula in two areas and created circumstances leading to the biogeographical patterns of the present day. The Vail global eustatic curve, supported by the oxygen isotope record, indicates that sea levels were c. 100 m above the present-day level during the early/middle Miocene (24-13 Ma) and again during the early Pliocene (5.5-4.5 Ma). Present topography suggests such high sea stands would have created 30-100-km wide seaways north and south of the Nakhon si Thammarat Range in the central peninsula (southern Thailand). Geological, palaeontological and phylogenetic evidence for such hypothetical seaways is scant (there have been no focussed searches) but does not preclude their occurrence. The role of such Neogene highstands in explaining present day biogeographical patterns in Southeast Asia and elsewhere requires assessment.