Sunda region, located in the tropical region of Southeast Asia, is one of the three main regions of the tropical rainforests with the highest biodiversity in the world, and also the most endangered ranges of species extinction. The high biodiversity in the region was due to several reasons: ①the lucky geographical location in the warm and moist tropics, ②joint zone between the two large tectonic plates Eurasia and India-Australia, ③with abundant of islands separated with different distances. ④In the cycles of glacial-interglacial during the geological history, the variations of the temperature and the fluctuations of the sea level created opportunities for the species interactions and gene mixture, therefore resulting in the formation of new species and contributing more species to the region. In particular, during Quaternary period, the continental shelves exposed repeatedly during the glacial times, and the many islands were often merged into one or a few continuous and large territories, making the gene flows within species easier. During the interglacials, the sea-level rose and the continental shelved were submerged, and the scattered and isolated territories might make the speciation and extinction occurred more frequently. Biological refugia might be important for many species’ survival. Today, with the rapid global warming and intensive human disturbance, the refugia may be more crucial for many species to survive. However, the extinction of many species may be inevitable.