Formation History of the Japanese Islands
The Japanese Islands have been independent of the Asian continent since the Sea of Japan started expanding 20 million years ago. Before the separation of the islands, the basement of Japan was formed in the margin of the continent. The Japanese tectonic history from the past through the future can be divided into three stages: a period of passive (Atlantic type) continental margin (700 to 500 million years ago), period of active (Pacific type) continental margin (500 million years ago to 50 million years later), and period of collision and assimilation to a continent (after 50 million years later). The history of the Japanese Islands corresponds with the lifetime of the Pacific Ocean (Isozaki, 2000).
Keys to understand the history
Fig. 1 Basement geologic map 
Pre-Neogene accretionary complexes and metamorphic rocks constitute
the Japanese island arcs as basement rocks, covered with Neogene and
Quaternary deposits and volcanic products. The basement rocks have
information related to the origin and evolution of the Japanese Islands.
Accretionary complexes, regional metamorphic rocks and granites that
were formed in a subduction zone 500 million years ago and later compose
more than 90% of the basement rocks. Rocks other than these rocks
include ultrahigh pressure metamorphic rocks and Paleozoic shelf
sediments, which are different from rocks formed in the subduction zone
and considered as fragments of continental blocks. These minor rocks are
distributed in the Hida Belt and the South Kitakami Belt,
including rocks more than 500 million years old. Some of the rocks are
similar to rocks found in China and the Korean Peninsula. Also, rocks
resembling main component rocks of the basement occur in the Asian
Since an accretionary prism develops seaward (outward), an accretionary complex on the forearc (trench) side is younger than that on the backarc side (see section “Accretionary prism”). In the Japanese Islands, the characteristics of accretionary complex are well preserved in southwest Japan. Accretionary complexes and metamorphosed accretionary complexes are zonally distributed in parallel to the Nankai Trough, becoming younger toward the Pacific Ocean. It is thought that the geotectonic frame work of southwest Japan extends to the Nansei Islands to the south of Kyushu. The distribution pattern of basement rock units in northeast Japan differs from that in southwest Japan, which is demonstrated by unclear zones obliquely across the island arc (not parallel to the trench). This pattern probably resulted from the change of the original geotectonic structure during the formation of the Sea of Japan in the Miocene epoch. Therefore, the basement rock units in northeast Japan can be correlated with those of southwest Japan. The basement rock units in Hokkaido are distributed north-south. It is thought that tectonic settings of the areas in which the basement rocks of Hokkaido were formed differed from southwest and northeast Japan. However, the geotectonic zone [the North Kitakami (Oshima) Belt] in western Hokkaido belongs to northeast Japan.
The above facts show that the basement of Japan has been developed toward the outside (trench side) in the subduction zone in the margin of the continent for about 500 million years. However, it seems that the growth of the Japanese island arcs has not been constant in their history. See “Continental crust and development of island arcs” (Japan in a subduction zone) and “Vanished granitic batholiths” below.
Fig. 2 Succession of ophiolite
Ophiolite occurs in some small areas in Japan. Ophiolite is bedded complex, the succession of which consists mainly of peridotite, gabbro, dolerite, basalt, and pelagic sediments including chert in this order from the bottom. These are remnants of uppermost mantle and oceanic crust. Paleozoic, Mesozoic, and Cenozoic ophiolites are found in Japan. Ophiolite occurring in Nagasaki Prefecture is the oldest, 580 million years old. Although the distribution of ophiolite is limited areas, ophiolite possessing information of the oceanic crust is important rock to know the geological history of Japan.
Zircon chronology is a dating method using radiometric dating of zircon (silicate mineral). Zircon is widely found in igneous rocks and also in sedimentary rocks (detrital grains) and metamorphic rocks. Zircon is hardly altered and metamorphosed, preserving the primary condition of crystal growth. Therefore, zircon chronology is very useful for dating of sedimentary rocks without fossils and original rocks of metamorphic rocks (protolith) because of difficulty in their dating with different methods. Recently, debris zircon chronology has suggested new facts in the history of the Japanese Islands (mentioned later).
• I recommend that you get the following article to see paleogeographic maps and figures related to the history of the Japanese Islands. This article is written in Japanese but includes English descriptions of figures. It is available in a page of the J-STAGE's website (PDF file).
Isozaki et al. (2011), Growth and Shrinkage of an Active Continental Margin: Updated Geotectonic History of the Japanese Islands [Journal of Geography (Chigaku Zasshi) Vol. 120, No. 1, P65-99"].
• The following sections are also helpful in understanding the history: “Japan in a Subduction Zone” (Accretionary prism, Metamorphic rocks) and “Outline of landforms and geology”.