Hidden Kingdom: Japan's Christian Martyrs, the Englishman Who Could Never Leave, and Two Hundred and Fifty Years of Deliberate Isolation
In 1614, Japan's shogun ordered every Christian priest expelled, every church demolished, and every convert to renounce their faith or die. What followed was one of the most systematic religious persecutions in history — lasting most of the seventeenth century, producing thousands of martyrs, and driving the remainder underground. Then, in 1865, missionaries returning to Japan discovered something extraordinary: communities of secret Christians near Nagasaki who had kept their faith alive for two hundred years without priests, without churches, passing prayers and the rite of baptism from parent to child in silence.
By BookOfWorldHistory·June 2, 2026·History·12 min read · 2,352 words
Originally published at: https://www.bookofworldhistory.com/blog/japan-christian-martyrs-will-adams-hidden-kingdom-feudal-society
In 1614, Japan's shogun ordered every Christian priest expelled, every church demolished, and every convert to renounce their faith or die. What followed was one of the most systematic religious persecutions in history — lasting most of the seventeenth century, producing thousands of martyrs, and driving the remainder underground. Then, in 1865, missionaries returning to Japan discovered something extraordinary: communities of secret Christians near Nagasaki who had kept their faith alive for two hundred years without priests, without churches, passing prayers and the rite of baptism from parent to child in silence.
The persecution began in stages. Ieyasu, the shogun who consolidated the Tokugawa dynasty, issued an edict in 1606 forbidding further Christian conversions and ordering the new teaching to be abandoned. Almost nobody obeyed it. In Nagasaki — by that point effectively a Christian city — a magnificent procession marched through the streets in honour of Ignatius Loyola, the founder of the Jesuit order, practically in defiance of the edict.
Ieyasu noticed.
For the next several years he tightened the pressure on Christians in and around his own court, while allowing the broader situation to continue. Then, in 1614, he made a final decision. All foreign priests were to be expelled. All churches were to be pulled down. Every Japanese Christian was to publicly renounce their faith or face the consequences. The edict was posted on public notice-boards, where it remained for over two and a half centuries — not removed until 1868.
The persecution of Japanese Christians began in earnest in 1614 under Shogun Ieyasu — churches demolished, priests expelled, and converts required to publicly renounce their faith or face execution. The edict remained on public notice-boards until 1868.
What the Persecution Actually Did — Street by Street, House by House
The methods used against the Christians of Japan were thorough and, in their thoroughness, deeply calculated. Rewards were offered to informers — rising as high as three hundred pieces of silver for the discovery of a Christian who had previously renounced the faith and then returned to it. Whole families were held responsible for individuals: if a priest was found hidden in a house, everyone in the house died. Parents who refused to inform against Christian children, children who refused to inform against Christian parents — all shared the same fate.
The most intensive operation was aimed at Nagasaki. In 1626, that city still had an estimated forty thousand Christians. The governor sent to clear it divided the city methodically: streets sealed at night by gates, each street under a headman responsible for every household, each group of five houses under an overseer who was expected to know the name and occupation of every person inside. The entire city became, effectively, a surveillance apparatus. The governor worked through it block by block.
Those who refused to recant were handed to the torturers. A method specific to this governor used the local geography: his prisoners were brought to a spot where natural boiling springs rose from the ground. Their backs were cut open, and the boiling water poured in. Other methods available to the persecution included burning, crucifixion, beheading, being torn apart by oxen, being sewn into rice sacks that were then set alight, and being starved to death in cages with food placed in view.
By 1627, there was reportedly not a single avowed Christian left in Nagasaki. The governor had killed or broken or exiled the entirety of a forty-thousand-person community in approximately a year.
The Torment of the Fosse — The Worst They Found
The persecution's investigators eventually developed what they considered their most effective instrument: a pit.
The martyr was hung upside-down in a deep hole, suspended by a rope tied about the feet, head downward. European observers who interviewed survivors — people who had endured it and then recanted and been pulled out — were told by those people that nothing else they knew of compared to it. Not burning. Not any other form of torture. The inversion caused the blood to press continuously against the brain in a way that produced an agony that was also uniquely prolonged. Martyrs executed by fire died quickly. In the fosse, men lasted eight or nine days.
A young woman held out for fifteen days and died without making the signal that would have brought her immediate release.
Alongside the fosse, the authorities developed another instrument of detection: trampling on the cross. A crucifix was placed on the ground and every member of every household was required to step on it. Refusal was immediate identification as a Christian. Infants too young to walk were carried to it by their mothers and their feet pressed onto the image.
What Survived — Two Hundred Years in Silence
The Japanese government, by the end of the seventeenth century, believed it had finished the work. Christianity had been destroyed. The evidence appeared to support this: no churches, no priests, no public practice, no visible community. The persecution had succeeded.
It had not succeeded entirely.
In 1865, Catholic missionaries returning to Japan — permitted by that point under pressure from European powers — discovered, in the villages around Nagasaki, communities of people who were still Christian. They had no priests. They had no churches. They had almost no books. What they had were prayers memorised and passed from parent to child across generations, and the rite of baptism preserved in the same way. For more than two hundred years, with no institutional support of any kind, small communities had maintained a private practice so careful and so quiet that the systematic investigations of the shogunate had not found them.
The Japanese government's response to the 1865 discovery was to post a new edict. The evil sect called Christian, it read, is strictly prohibited. Suspicious persons should be reported to the proper officers, and rewards will be given. A number of the rediscovered Christians were seized and exiled to distant provinces.
This time, European powers intervened with enough diplomatic force to make the edicts unsustainable. In 1872, the exiled Christians were permitted to return. Religious persecution as official policy in Japan ended there.
In 1865, missionaries in Japan discovered Christian communities near Nagasaki who had maintained their faith in secret for over two hundred years — passing prayers and the rite of baptism from parent to child with no priests, no churches, and no institutional support of any kind.
Will Adams — The Englishman Japan Would Not Release
In 1598, a Kent-born pilot named Will Adams sailed from Holland as chief navigator of a five-ship Dutch East India Company fleet heading for the East Indies by way of the Straits of Magellan. Of the five ships, two turned back at the straits. A third was captured by the Spanish. The remaining two — the Hope and the Charity — crossed the Pacific.
The Hope disappeared. Its fate was never determined.
The Charity, Adams at the helm, made it across, but barely. Scurvy had devastated the crew until the ship could no longer be properly handled. When it finally reached the Japanese island of Kyushu, only four men aboard could stand upright. Adams was one of them. Four more could move on hands and knees. The rest were helpless.
The local governor received them with reasonable care, though much of their cargo was plundered by locals. Then some Portuguese traders arrived from Nagasaki — and rather than helping their fellow Europeans, the Portuguese, who were commercial rivals of the Dutch and bitterly hostile to them, told the Japanese governor that the Dutch sailors were pirates and should be put to death.
The case was referred to the shogun Ieyasu, who summoned Adams to appear before him. Adams was then held in prison for thirty-nine days expecting at any moment to be crucified — the standard execution method for pirates. Ieyasu, however, questioned Adams at length, understood that the Dutch-Portuguese enmity was a European affair of no relevance to Japan, and declined to execute men who had done him no harm.
He released Adams. Then he kept him.
Will Adams arrived in Japan in 1600 as the barely-surviving pilot of a Dutch ship, was held for thirty-nine days expecting execution, and then found himself kept at the shogun's court for the rest of his life — given a feudal estate, a Japanese wife, and the Japanese name Anjin-Sama: Mr. Pilot.
Anjin-Sama — Mr. Pilot, Lord of an Estate, and Never Going Home
Ieyasu was a practical man. He saw in Adams something useful: a skilled navigator, an honest informant about European affairs, and a man who could mediate between Japanese interests and the foreign traders increasingly appearing on the coast. He made Adams a court fixture and refused all requests to let him go.
Adams built ships for the shogun — Western-style vessels that delighted Ieyasu. He acted as intermediary between the Japanese government and Dutch and later English traders. He had long conversations with Ieyasu about European politics and the state of the world. When Dutch ships appeared off the coast in 1609, Adams helped them gain trading rights, siding with his old Dutch employers against Portuguese attempts to block them. Two years later, English traders arrived and Adams helped them secure a charter to trade in any Japanese port.
For all of this, he was well rewarded. Ieyasu gave him a substantial rural estate — described in Adams's own letters as a living like unto a lordship in England, with eighty or ninety husbandmen as servants. An English visitor who saw the estate in 1616 described it as having over two hundred farms, with Adams holding effective power of life and death over the people on it. He had a house in Edo near the shogun's court. A street there was called Pilot Street in his memory, and his Japanese name — Anjin-Sama, Mr. Pilot — became the name by which he was known throughout Japan.
He married a Japanese woman and had children with her, while his English wife and the children he had left at home in Kent remained a source of grief he mentioned repeatedly in his letters. He never returned. He died in Japan in 1620.
The Japanese honoured him as the founder of their naval tradition. He was made a Shinto divinity under the name Angin-Haka. Flowers are still placed on his tomb.
The Sealed Country — Japan's Two Hundred and Fifty Years of Chosen Isolation
The reasoning behind Japan's self-imposed isolation was not irrational. Japanese rulers had watched what European contact was doing to other parts of Asia: trade followed by missionaries, missionaries followed by political interference, political interference followed by colonisation. The sight of Portuguese and Spanish activities elsewhere in the Pacific was available to any informed Japanese observer, and what it suggested was not reassuring.
The shogun Iemitsu, third of the Tokugawa line, made the definitive decision in the 1630s. Every port was closed except Nagasaki, where Dutch traders were permitted to operate from a small artificial island under strict conditions — kept separate from the Japanese population, their movements controlled, their activities monitored. No other European nation could approach Japan at all. Japanese subjects were forbidden from travelling abroad. Ocean-going vessels — ships capable of crossing open water — were destroyed. What remained were coastal craft that could creep along the shoreline, sometimes taking a year to cover a few hundred miles.
For approximately two hundred and fifty years, this held. Japan developed in isolation — its feudal institutions intact, its culture continuing to evolve in its own direction, its technology frozen roughly where it had been when the gates closed. When the isolation ended in the mid-nineteenth century, the world that came through the door was carrying breech-loading rifles and rifled artillery. Japan had bows and matchlocks of fifteenth-century design.
The gap this created, and the speed with which Japan then moved to close it, is one of the more striking stories in modern history — but that belongs to a different chapter.
The Feudal Rules — What You Could Wear, What You Could Eat, and Whether You Could Use an Umbrella
Inside the sealed country, the Tokugawa feudal system ran with a precision that touched every detail of daily life. The social hierarchy was fixed and enforced: Daimyo at the top, then Samurai, then farmers, craftsmen, merchants. Each class operated under rules specifying exactly what its members could and could not do, own, wear, eat, and give as gifts.
A farmer whose land yielded a hundred koku of rice a year could build a house sixty feet long, but it could have no parlour and the roof could not be tiled. If he feared fire and wanted tiles instead of thatch, he had to apply for permission first. His family could not wear silk. If a child married someone of a class that permitted silk, the farmer was required to ask that person not to wear silk at the wedding. At funerals, no wine could be offered to visitors. The permitted wedding menu was specific and modest. Even grandparents giving presents to grandchildren at children's festivals were regulated: no dolls for the girls, no toy flags for the boys — small money gifts only.
For labourers, the rules were stricter still. The house must be thatched, no exceptions. A feast might offer one dish and one soup, but not in cups. A wife might own a silk sash but could not wear it in public. And the labourer was not to use an umbrella except in genuine necessity, since a straw raincoat was, in the eyes of the law, sufficient for his station.
The government accompanied these rules with an explanation of their intent — that they existed not to oppress but to prevent families from spending beyond their means, to maintain social order, and to encourage frugality. The explanation had the characteristic quality of all such explanations: it was not entirely false, and it was also not the whole story.
The Eta — Japan's Untouchables
Below the four official classes — Samurai, farmers, craftsmen, merchants — was a group not counted as part of the population at all. The Eta were Japan's outcast class, and their position in Japanese society was absolute in a way that made European concepts of the outcast look moderate.
They were not permitted to live near other people. Their villages were excluded from road measurements — the highway simply did not officially pass by where they lived. Ground where an Eta had stood was considered polluted and had to be sprinkled with salt before a Japanese person could walk on it. A Samurai who killed an Eta for a slight thought no more of it than killing a dog. The poorest labourer in Japan considered it an insult to be placed in the same social category as an Eta.
The work reserved for them matched their status: slaughtering and skinning animals, executing criminals, disposing of bodies. Many were tanners and shoemakers. Their own internal community had headmen and a chief who lived in Edo and, by tradition, was permitted the two swords that marked Samurai rank.
Where they came from is not agreed upon. Theories include Korean prisoners of war, Mongol captives from Kublai Khan's defeated invasion force, or — the most widely accepted modern view — a class that gradually formed from those whose occupations under Buddhist doctrine involved taking life, rendered ritually impure by their work until the impurity became permanent and hereditary.
In 1871, a legal decree placed the Eta formally equal to other Japanese citizens. In practice, the adjustment took longer. A school built with Eta money opened to no students the first day — no Japanese family would send their children. The breakthrough came when the local district governor — a Samurai — enrolled himself as a pupil and the night before opening slept at an Eta family's house. The school filled after that. Legal equality and social reality do not always travel at the same speed.