The land that would go on to form the Nansei Islands was lifted up by volcanic activity 15 million years ago. Until 10 million years ago, this land was connected to the Japanese island of Honshu and the Eurasian continent because of low sea levels during a glacial period. Accordingly, various flora and fauna including mammals, reptiles, insects, and plants made their way over. However, around two million years ago, the climate began to warm, resulting in higher sea levels. The 160 Nansei Islands emerged across a span of about 1,200 kilometers from south of Kyushu to Taiwan. The plants and animals stranded on the islands followed unique evolutionary paths, forming ecosystems adapted to the environment of each island. This is why even though the islands have identical origins, each is home to diverse endemic species due to differing environmental conditions, such as differences in latitude and island size.

The Iriomote cat is a species of wildcat that lives only on Iriomotejima Island in Japan. It is thought to be related to the leopard cat found on the Eurasian continent. It is a rare species at risk of extinction, with the current population consisting of only about 100 individuals, and intense conservation efforts and ecological studies are underway.

Iriomotejima was first settled during the Jomon period (around 14,000 to 300 BCE), as evidenced by shell heaps discovered throughout the island. However, with frequent outbreaks of malaria, permanent settlement is thought to have faced challenges. The island retains its own unique culture, as exemplified by the Shichi Festival, a religious tradition that blends Okinawa's indigenous nature worship with Buddhism, which arrived later from the continent.

The Yanbaru region consists of the three villages of Kunigami, Ogimi, and Higashi in the northern part of Okinawa Prefecture. It is a forested region containing mountains 400 to 500 meters in elevation. It is home to many endemic species with origins in other parts of Asia, including the Okinawa rail, which is thought to be closely related to the barred rail found in the Philippines and Indonesia, and the Yanbaru long-armed scarab beetle, a subspecies of the long-armed scarab beetles also found in mainland China. The rich natural environment of Yanbaru makes it a paradise for these species, which could not have survived elsewhere.

Although lifestyles based on hunting and gathering predominated on Okinawa Island until the tenth century, agriculture began during the twelfth century, and the Ryukyu Kingdom was founded around the fifteenth century. It prospered greatly by trading with Japan and other Asian countries, creating a unique Ryukyu culture. However, it was invaded by Satsuma Domain in what is now Kagoshima Prefecture in 1609 and became a vassal state. Later, it was made part of Japan as Okinawa Prefecture in 1879.

The Nansei Islands of Amami Oshima and Tokunoshima are known as the Central Ryukyus. Since no carnivorous mammals have lived on these islands since their separation from the Eurasian continent, small animals such as the Amami rabbit, the Ryukyu spiny rat, and the Amami Ishikawa's frog have followed unique evolutionary paths, and the islands are home to numerous endemic species. In addition, even though these islands only account for about 0.2% of Japan's landmass, they are home to about 13% of its identified species, making them astonishing hotspots of biodiversity.

Amami Oshima and Tokunoshima had a unique southern-island culture different from the Jomon culture on the main islands of Japan. Archaeological sites dating back until about 7,000 years ago have been discovered throughout the islands. According to the ancient Japanese chronicle Nihon Shoki, trade was flourishing around the seventh century. Starting during the fifteenth century, culture developed with influence from the Ryukyu Kingdom and Satsuma Domain. After the Meiji Restoration of 1868, the islands were incorporated into Kagoshima Prefecture.