According to the Irosetsuden, the name of Naha comes from its original name, Naba, which was the name of a large, mushroom-shaped stone in the city. Gradually, the stone wore away and became buried, and the name's pronunciation and its kanji gradually changed.
In Naha, some archeological relics of the Stone Age were found. From a Jōmon period kaizuka (shell mound), ancient Chinese coins were found. Pottery found by archaeologists indicates that the area was an active site of trade with the Japanese archipelago and Korean peninsula at least as early as the 11th century. Though it is not known just when the area first became organized as a functioning port city, it was active as such by the time of the unification of the Ryūkyū Kingdom in the early 15th century.
Though today Naha has grown to incorporate the former royal capital city of Shuri, center of Chinese learning Kumemura, and other towns and villages, in the period of the Ryūkyū Kingdom, it was a smaller city, prominent as a major port, but not as a political center.
Medieval Naha was on a tiny island called Ukishima, connected to the mainland of Okinawa Island by a narrow causeway called which led on to Shuri. The main port area for international trade, Naha proper, was divided into the East (東, higashi) and West (西, nishi) districts and was on the southwestern portion of Ukishima. A large open-air marketplace was active in front of the royal government trading center, or oyamise (親見世). A number of Japanese temples and shrines were located here, along with a residence and embassy, known as the Tenshikan (天使館), for visiting Chinese officials. A pair of forts (Mie gusuku and Yarazamori gusuku) built atop embankments extending out across the entrance to the harbor defended the port, and a small island within the harbor held a warehouse, Omono gusuku (御物グスク), used for storing trade goods.
Tomari (泊), on the mainland of Okinawa Island to the northeast of Ukishima, served as the chief port for trade within the Ryūkyū Islands. The administrators of Tomari were also responsible for collecting and managing the tribute paid to the kingdom by the Amami Islands, whose tribute ships made port here.
Major sites in the community included the Tensonbyō Taoist temple near the northern end of Kume-Ōdōri and two shrines called Upper and Lower Tenpigū, dedicated to the Taoist goddess of the sea Tenpi, also known as Matsu. A Confucian temple, the gift of the Kangxi Emperor, was built in Kumemura in the 1670s; the Meirindō, a school of classic Confucian Chinese learning, was established in 1718. Following their destruction in World War II, the Meirindō, Confucian temple, and Tenpigū shrines were rebuilt on the site of the Tensonbyō in northern Kume, where they stand today as the Confucian temple Shiseibyō.
On the northwest side of Ukishima lay, a community traditionally said to have been founded by Japanese settlers. It was organized around Wakasamachi-Ōdōri, an avenue which intersected with Kume-Ōdōri and ran across tidal mudflats to the east of Ukishima, connecting the community to the port of Tomari on the Okinawan mainland. A number of Japanese shrines and temples were located in Wakasamachi, including the Naminoue Shrine, the Zen temple Kōganji, and temples devoted to Ebisu and Jizō. The community had lodgings specifically set aside for traders and travelers from the Tokara Islands.
Another settlement, known as Izumizaki, lay on the mainland of Okinawa Island, just across the Kumoji River from Ukishima. Izumizaki had no notable or major port facilities and is believed to have been simply an extension of the residential community of Naha proper, which thus spread onto the mainland as the population and according demand for land grew. At some point, the tidal mudflats and Kumoji River separating Ukishima, that is, Naha, from Okinawa Island were filled in. The neighborhoods of Kume, Wakasa, and Tomari can still be found in Naha today.
Commodore Matthew C. Perry's expeditionary squadron stopped in Naha en route to Tokyo in 1853; and the American ships visited several more times. The lithographs prepared from drawings made by the expedition's official artist would be widely circulated. These images would provide the basis for 19th century impressions of the geography and people of the Ryūkyū islands.
After the replacement of the Ryūkyū Kingdom with the Ryūkyū Domain in 1872, Naha became the capital city. The Ryūkyū Domain was abolished in 1879 and the former Ryūkyū Kingdom came to an end, fully annexed by Japan as Okinawa Prefecture, with Naha remaining as the capital city. Shuri and other neighboring municipalities were absorbed into the city.
On April 1, 2013, Naha became a core city, a category of cities of Japan under the Local Autonomy Law of Japan. Naha now carries out many of the functions, notably for public health care, normally delegated to the prefectural government. Naha is the first core city in Okinawa Prefecture.
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