In the Quaternary, the Ryukyu Islands evolved from a continental margin arc to an island arc by backarc spreading of the Okinawa Trough, accompanied by subsidence and isolation of the islands, a process that has continued to the present. Trough-parallel half grabens were filled with marine siltstone. Similar sediments filling orthogonal fault-controlled and west-draining non-tectonic valleys record island separation. New Quaternary nannofossil biostratigraphic data date the deposition of the marine siltstone at 1.552 ± 0.154 Ma. At that time, the entire 1000 km-long island chain comprising the Ryukyu Islands separated from the Asian continent by rifting extending from the Okinawa Trough to the Tsushima Strait. The Tokara, Kerama, and Yonaguni gaps, branched or transverse rifts of the Okinawa Trough, separate the island chain into subgroups of the Osumi, Amami, Okinawa, and Yaeyama islands, and Taiwan. The shallow Taiwan Strait separated Taiwan from the Chinese mainland. The Kuroshio warm current that previously ran offshore of the continental margin arc began to enter the opening backarc basin through the Yonaguni gap and to exit through the Tokara gap, flowing along the axis of the Okinawa Trough. Under influence of the warm current and because of entrapment of continentally sourced detrital sediments by the Okinawa Trough, coral reefs formed around each island. These reefs make up a unit called the Ryukyu limestone. Subsidence continued through the deposition of this limestone, resulting in further isolation of each island. Some islands did not separate from the mainland but emerged above sea level later as a result of volcanic edifice construction or forearc uplift. Following initial isolation, the Japanese islands and Taiwan may have been connected to the mainland by land bridges during some sea level low stands related to glacial periods, whereas the other islands remained isolated. Based on ages of isolation of each island, a Quaternary palaeogeographic map and ‘phylogenetic tree’ of the islands can be drawn showing the separation time of each island from the mainland and from each other. This information should be useful for phylogenetic molecular biologists studying evolution of Ryukyu endemic species and vicariant speciation and could facilitate analysis of the DNA substitution rate.