The history of Kumamoto Prefecture has been documented from paleolithic times to the present. Kumamoto Prefecture is the eastern half of Hinokuni (meaning "land of fire"), and corresponds to what was once called Higo Province. Exceptions are the parts of Kuma District, which had once been part of Sagara Domain, and Nagashima which was included in Kagoshima Prefecture.

Kumamoto Prefecture is roughly divided into three areas, namely, the northern area with Kikuchi River, Shirakawa River and Mount Aso Area; the Kumagawa Area including the Hitoyoshi Basin and the Amakusa Island Area. The first one is the Kumamoto han, and the second the Hitoyoshi han and the third one is the Amakusa Area, once controlled by the Tokugawa shogunate.

The history of Kumamoto is characterized by kofuns in natural beauties or volcanic activities, the ritsuryō and the following rise of samurais, the arrival of Katō Kiyomasa from Nagoya, wars around the Bakumatsu including the Satsuma Rebellion, and public problems concerning Minamata disease. After the establishment of the Yamato Government or Yamato Ouken, the history of Kumamoto has been constantly under the influence of the Central Government.

Prehistoric Kumamoto About one-third of the archaeological sites of the Lower Paleolithic age in Japan were found in Kumamoto Prefecture. A few of these have been excavated. Mainly these were in the outer Aso mountain areas and Kuma district. The oldest one is the Ishinomoto Site in Hirayama machi in Kumamoto City; dating back more than 30,000 years ago by the radiocarbon dating method. A large number of artifacts or stone tools such as stone axes and knives were excavated, suggesting that Kyūshū was inhabited by a number of hunter-gatherer societies.

At the same time, Kyūshū experienced volcanic activity at Mount Aso, Aira Caldera in Kagoshima Prefecture and Kikai Caldera. There were four large series of Mount Aso volcanic eruptions, with structural changes. The last one was about 90,000 years ago. The lava produced stone materials that would later be used for bridge construction in the Prefecture.

Jōmon period and Yayoi period

Jōmon period

There is little evidence of human activity in the early part of the Jōmon period in the Kumamoto Prefecture, because of volcanic activity about 7300 years ago by the Kikai Caldera in Kagoshima Prefecture. The Goryo midden and Kurohashi midden date to the middle age of the Jōmon period. Later, 13 middens in Kumamoto were situated at the height of 5 meters above sea level. In Souhata midden, stored acorns were found. Fish hooks made of stone were found in Amakusa. A peculiar style of earthenware called kokushokukenmadoki was developed according to the development of living styles. Burned rice corns and barley corns were found in a dugout (shelter) dwelling in Uenobaru midden in Kumamoto City.The History of Kumamoto City 770 Archaeological sites were found in the Jōmon period in Kumamoto Prefecture, including Kannabe midden, Kumamoto in which Dogūs and ground stones were found.

Yayoi period

In the Yayoi period, there appeared dwellings in ring-formed groups in which onggis, tsubo jars, and stone axes were found. Dwellings rose into higher places, moving from the seashores. Cultivation and agriculture started in the Yayoi period, because the Kumamoto plain started to rise because of stream sediments from the rivers. Cultivation of rice started, while there were shell heaps along the seashore. Salt was produced by burning sea weeds; which has been verified by the presence of burned small seashells. In later years, there were middens with ironware along the Kurokawa river, Shirakawa river, and Kikuchigawa River and in the Futagozuka midden in Kumamoto City, suggesting the production of ironware there. In the Yayoi period, there were 740 middens in Kumamoto Prefecture, comprising 13% of middens in Japan. In the Tokuo midden and the Kogabaru midden, bronze mirrors were excavated.

Land of Fire

In the Nihon Shoki, Japan's earliest official document, the early countries of Yamato Ouken, Wa (Japan), appointed a king of a small area which came under the Yamato Ouken, a head of Agata Nushi (an agata was an autonomous district under the leadership of a chieftain or warlord). Yamato Ouken is considered to be the forerunner of Japan's Imperial House of Japan existing in the Nara area or somewhere and started in the 3rd century. In the same document and in the Chikushi-koku-fudoki, there were three Agatas or Districts in the present Kumamoto Prefecture: Kuma agata, corresponding to Kuma Area; Asonken, corresponding to the Mount Aso area; and Yatsushiro area, which is considered to have been larger than today.

There are about 1,300 Kofuns in Kumamoto Prefecture, and comprise 24% of kofuns in the country. Near the Uto Peninsula area are about 120 large kofuns, or megalithic tombs or tumuli, constructed between the early 3rd century and early 7th century. In Kumamoto Prefecture, there is a concentrated distribution of decorated kofuns, in which various patterns were drawn, for instance, breasts of a woman in Chibusan kofun in Yamaga city. In another kofun in Uto city, the burial of a woman in her thirties was confirmed, suggesting the presence of miko, a "female shaman, spirit medium" who conveyed oracles from kami. A sword in a kofun named Etafunayama kofun had Chinese characters describing Emperor Yūryaku. Because of this, historian Wakatakeru has suggested that this area was under the control of Yamato Ouken. One of the gōzokus was named Takebe-no-Kimi, a family of samurai nature, who was given such a name by Yamato Ouken, and who was assumed to live near Kokai-Honmachi; in those days, near Takebe.

A group of kofuns at Nozu are considered to be the site of Hinokimi or the King of fire or possibly King of the Hi River. Hinokimi was considered to be a descendant of one who answered to Emperor Keikō. In the mythological period, Emperor Keikō in his journey for expanding the Yamato Ouken, saw unexplainable spots of moving fire, Shiranui, (In Japanese, literally "unknown fire") in the Ariake Sea, and a Gozoku in that land replied that he did not know the fire. Today, it can be seen only on one day or so, and it is an optical phenomenon on the horizon of seeing moving spots of fire caused by fishing boats through heated air layers. See also Shiranui (optical phenomenon).

In 527AD, the Iwai Rebellion in Fukuoka Prefecture was quelled by the Yamato court. The rebellion was named after its leader, Iwai, who is believed by historians to have been a powerful governor of Tsukushi. The rebellion was quelled by the Yamato court, and played an important part in the consolidation of early Japan. The eruption of Mount Aso was described in the Book of Sui, probably through the influence of Yamato Ouken.

The rise of the Samurai In the latter part of the Heian period, groups of samurai gained power. This was also so in the land of Higo, though unification was not achieved until the 16th century. Well known groups of samurai included the Kikuchi clan, Aso clan, Kihara of the Midorigawa area, Moroshima of Amakusa, Sagara clan of Hitoyoshi, and Kumabe; some of them fought in the Toi invasion of 1019.

Kikuchi Clan

The Kikuchi clan started with Fujiwara Noritaka, grandson of Fujiwara no Takaie, who fought in the Toi invasion. However, at present, there are several views concerning its origin; 1) Local Gōzoku who worked at Dazaifu, Fukuoka Prefecture, 2) A descendant of Kishitsu Fukunobu from Korea, 3) A descendant of the Kukuchi family, 4) A descendant from the Minamoto clan. The Kikuchi clan enjoyed a powerful presence in the Kikuchi area, belonging to the group in the center of Japan by maintaining their land in the shōen system. In the days when the Taira clan was in power, the Kikuchi clan approached the Taira clan, but then the Minamoto clan came to power, and the Kikuchi favored the Minamoto. In the Kamakura period, the Kikuchi clan fought successfully against the enemy at Fukuoka during the Mongol invasions of Japan. Kikuchi Taketoki (1292–1333) was the 12th head of the Kikuchi Clan. Emperor Go-Daigo asked Taketoki for help. He was Go-Daigo's first man and was awarded for this. Taketoki gathered many people in Kyūshū and planned to attack Chinzei Tandai's Hōjō Hidetoki (Akahashi Hidetoki), but the plan was discovered and the Hojo attacked first. Taketoki and his son Yoritaka died in this attack. However, the Kikuchi clan remained powerful in this area.

Aso Clan The Aso clan started with Kannushi worshiping the kami of Mount Aso area and later became the head of the Agata by presenting their land to the Yamato Ouken and later to the group in power as an organized manor (shōen). They became a powerful group of samurai, and they named themselves a Dai-guji, or great Kannushi and the top of gōzokus or samurai combined. It is said that Aso Shrine was the earliest shrine in Higo Province and included lower shrines such as Kengun Shrine in Kumamoto, Kosa Shrine, and Kouriura Shrine which extended the area of influence.

The formation of Samurai groups

Legend of Minamoto no Tametomo In the latter half of the Heian period, samurai had waged wars in almost all areas of Japan, and Shirakawa Jokyo in cloistered rule started to control kokushis; the situation became very complex. In Kyūshū, Minamoto no Tametomo, a hero from Kyoto, was the subject of a number of legends. The legend of Minamoto no Tamotomo was interpreted as the uprising of groups of samurai in rural or peripheral areas of Japan against the previously authoritative groups of samurai. When Taira no Kiyomori had power, smaller groups of samurai had to choose either to side with the Heike clan or resist. The Rebellion of Chinzei was recorded in the Azuma Kagami, The Tale of the Heike, Genpei Jōsuiki, and it coincided with the uprising of Minamoto no Yoritomo. Defeated, their groups were incorporated within the Heike clan.

Kamakura Shogunate and Mongol invasions of Japan The Kamakura period covers 1185 to 1333. Samurais in east Japan occupied the post of Soujitou, and the Kikuchi clan sided with Gotoba-joko, and lost to some extent. In 1268 and 1271, the Kamakura shogunate rejected the proposal of envoys from Mongol for peace. It ordered all those who held fiefs in Kyūshū to resist any Mongol Invasions. Fortunately Takezaki Suenaga left vivid pictures concerning the Mongol invasions of Japan.

Takezaki Suenaga

Takezaki Suenaga (1246–1314) was a retainer of Higo Province who fought in both campaigns against the Mongols. Suenaga commissioned the Mōko Shūrai Ekotoba, a pictorial scroll showing his own valor in war, composed in 1293. During the Mongol invasion of 1274. Suenaga fought at Fukuoka under Muto Kagesuke. Suenaga sold his horses and saddles in order to finance a trip to Kamakura, where he reported his deeds in battle to the shogunate. In order to receive rewards for valorous deeds from the bakufu, it was necessary for the deeds to be witnessed by others and reported directly. By his own account in the scrolls, Suenaga says, "Other than advancing and having my deeds known, I have nothing else to live for", showing that, first, he wanted to advance in terms of measurable money and rank, and that, just as importantly, he sought fame and recognition.

Muromachi period The Muromachi period is subdivided into the Nanboku-chō period and the Sengoku period.

Nanboku-chō period