In the mid-1630s, the peasants of the Shimabara Peninsula and the Amakusa Islands, dissatisfied with overtaxation and suffering from the effects of famine, revolted against their lords. This was specifically in territory ruled by two lords: Matsukura Katsuie of the Shimabara Domain, and Terasawa Katataka of the Karatsu Domain. Though the rebellion is cast by many historians as a religious uprising, this does not address the issues of the discontent from the famine and overtaxation. Those affected also included fishermen, craftsmen and merchants. As the rebellion spread, it was joined by masterless samurai who once served families such as the Amakusa and Shiki who used to live in the area, as well as former Arima and Konishi retainers. As such, the image of a fully "peasant" uprising is also not entirely accurate.
Shimabara was once the domain of the Arima lordly family, which had been Christian; as a result, many locals were also Christian. The Arima were moved out in 1614 and replaced by the Matsukura. The new lord, Matsukura Shigemasa, hoped to advance in the shogunate hierarchy, and so he was involved with various construction projects, including the building and expansion of Edo Castle, as well as a planned invasion of Luzon. He also built a new castle at Shimabara. As a result, he placed a greatly disproportionate tax burden on the people of his new domain, and further angered them by strictly persecuting Christianity. Even the Dutch, who had a trading post nearby and were anti-Catholic, were startled at the excessive degree of repression. These policies were continued by Shigemasa's heir, Katsuie.
The inhabitants of the Amakusa Islands, which had been part of the fief of Konishi Yukinaga, suffered the same sort of presecution at the hands the Terasawa family, which, like the Matsukura, had been moved there. Other masterless samurai in the region included former retainers of Katō Tadahiro and Sassa Narimasa, both of whom had once ruled parts of Higo Province.
The rebels laid siege to the Terasawa clan's Tomioka and Hondo castles, but just before the castles were about to fall, armies from the neighboring domains in Kyūshū arrived, and forced them to retreat. The rebels then crossed the Ariake Sea and briefly besieged Matsukura Katsuie's Shimabara Castle, but were again repelled. At this point they gathered on the site of Hara Castle, which had been the castle of the Arima clan before their move to the Nobeoka Domain, but was dismantled. They built up palisades using the wood from the boats they had crossed the water with, and were greatly aided in their preparations by the weapons, ammunition, and provisions they had plundered from the Matsukura clan's storehouses.
They then requested aid from the Dutch, who first gave them gunpowder, and then cannons. Nicolas Koekebakker, head of the Dutch trading station on Hirado, provided the gunpowder and cannons, and when the shogunate forces requested that he send a vessel, he personally accompanied the vessel de Ryp to a position offshore, near Hara Castle. The cannons sent previously were mounted in a battery, and an all-out bombardment of the fortress commenced, both from the shore guns as well as from the 20 guns of the de Ryp. These guns fired approximately 426 rounds in the space of 15 days, without great result, and two Dutch lookouts were shot by the rebels. The ship withdrew at the request of the Japanese, following contemptuous messages sent by the rebels to the besieging troops:
By April of 1638, there were over 27,000 rebels facing about 125,000 shogunate soldiers. Desperate rebels mounted an assault against them on April 4 and were forced to withdraw. Captured survivors and the fortress's rumored sole traitor, Yamada Uemonsaku, revealed the fortress was out of food and gunpowder.
On April 12, 1638, troops under the command of the Kuroda clan of Hizen stormed the fortress and captured the outer defenses. The rebels continued to hold out and caused heavy casualties until they were routed on April 15.
The Shimabara rebellion was the first massive military effort since the Siege of Osaka where the shogunate had to supervise an allied army made up of troops from various domains. The first overall commander, Itakura Shigemasa, had 800 men under his direct command; his replacement, Matsudaira Nobutsuna, had 1,500. Vice-commander Toda Ujikane had 2,500 of his own troops. 2,500 samurai of the Shimabara Domain were also present. The bulk of the shogunate's army was drawn from Shimabara's neighboring domains. The largest component, numbering over 35,000 men, came from the Saga Domain, and was under the command of Nabeshima Katsushige. Second in numbers were the forces of the Kumamoto and Fukuoka domains; 23,500 men under Hosokawa Tadatoshi and 18,000 men under Kuroda Tadayuki, respectively. From the Kurume Domain came 8,300 men under Arima Toyouji; from the Yanagawa Domain 5,500 men under Tachibana Muneshige; from the Karatsu Domain, 7570 under Terasawa Katataka; from Nobeoka, 3,300 under Arima Naozumi; from Kokura, 6,000 under Ogasawara Tadazane and his senior retainer Takada Matabei; from Nakatsu, 2,500 under Ogasawara Nagatsugu; from Bungo-Takada, 1,500 under Matsudaira Shigenao, and from Kagoshima, 1,000 under Yamada Arinaga, a senior retainer of the Shimazu clan. The only non-Kyushu forces, apart from the commanders' personal troops, were 5,600 men from the Fukuyama Domain, under the command of Mizuno Katsunari, Katsutoshi, and Katsusada. There was also a small number of troops from various other locations amounting to 800 men. In total, the shogunate's army was comprised of over 125,800 men. Conversely, the strength of the rebel forces is not precisely known. Combatants are estimated to have numbered over 14,000, noncombatants who sheltered in the castle during the siege were over 13,000. One source estimates the total size of the rebel force as somewhere between 27,000 and 37,000, a fraction of the size of the force sent by the shogunate.
After the castle fell, the shogunate forces beheaded an estimated 37,000 rebels and sympathizers. Amakusa Shirō's severed head was taken to Nagasaki for public display, and the entire complex at Hara Castle was burned to the ground and buried together with the bodies of all the dead.
The shogunate suspected that Western Catholics had been involved in spreading the rebellion and Portuguese traders were driven out of the country. The policy of national seclusion was made more strict by 1639. An already existing ban on the Christian religion was then enforced stringently, and Christianity in Japan survived only by going underground.
Another part of the shogunate's actions after the rebellion was to excuse the clans which had aided its efforts militarily, from the building contributions which it routinely required from various domains. Matsukura Katsuie committed suicide, and his domain was given to another lord, Kōriki Tadafusa. The Terazawa clan survived, but died out almost 10 years later, due to Katataka's lack of a successor.
On the Shimabara peninsula, most towns experienced a severe to total loss of population as a result of the rebellion. In order to maintain the rice fields and other crops, immigrants were brought from other areas across Japan to resettle the land. All inhabitants were registered with local temples, whose priests were required to vouch for their members' religious affiliation. Following the rebellion, Buddhism was strongly promoted in the area. Certain customs were introduced which remain unique to the area today. Towns on the Shimabara peninsula also continue to have a varied mix of dialects due to the mass immigration from other parts of Japan.
With the exception of periodic, localized peasant uprisings, the Shimabara Rebellion was the last large-scale armed clash in Japan until the 1860s.