Chapter One

The Argument That Might Have Worked

On the morning of 16 July 1647, the lookouts on the hills above Nagasaki spotted two European galleons sailing into the bay. The effect was roughly equivalent to a dead man walking through the front door and asking for his old job back.

Eight years had passed since the final sakoku edict of 1639 had banned every Portuguese vessel from Japanese waters under penalty of death. Seven years had passed since the last Portuguese who tried — a diplomatic delegation of seventy-four men from Macau — had been arrested, tried, and beheaded, with thirteen survivors sent home carrying a message that could not have been plainer: even if the King of Portugal himself came, he would lose his head. The Tokugawa shogunate did not deal in ambiguity. And yet here, glinting in the summer light off Kyūshū, were two well-armed Portuguese warships flying the royal standard of a king the Japanese had never heard of, carrying an ambassador they had not invited, proposing a deal they had already rejected.

The 1644–1647 Portuguese embassy to Japan is one of the great forgotten gambits of early modern diplomacy — a three-and-a-half-year odyssey that crossed three oceans, survived shipwreck, Dutch detention, typhoons, and the death of its own captain, all to deliver a single argument to the most paranoid government on earth. The argument was elegant: Portugal had broken free from Spain, the very power the shogunate feared most. A new dynasty sat on the throne. The old grievances were dead. Surely Japan could do business with this new, independent, definitively non-Spanish Portugal?

It was not a stupid argument. It might even have worked — if not for a clause the ambassador was forbidden to concede, and a conspiracy that had not yet been discovered.

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Chapter Two

The Sixty Years That Ruined Everything

To understand why two galleons were sailing into a harbour where Portuguese ships were supposed to be sunk on sight, you have to understand the catastrophe that preceded them — and the catastrophe before that.

Between 1580 and 1640, Portugal had effectively ceased to exist as an independent kingdom. When the last of the Aviz dynasty died without an heir, Philip II of Spain — a man who collected kingdoms the way other men collected paintings — absorbed the Portuguese crown into his own. The Portuguese called the next six decades their “Sixty Years’ Captivity,” which gives some indication of how they felt about the arrangement.

For the Estado da Índia, Portugal’s sprawling network of forts, factories, and trading posts strung across Asia and Africa, the Iberian Union was a rolling disaster. Philip’s decision to close the port of Lisbon to Dutch merchants — a move of staggering economic self-harm, given that the Dutch had been the primary distributors of Portuguese spices in northern Europe — drove the Netherlands to do the obvious thing: build their own fleet and take the Portuguese empire by force. Malacca, Hormuz, the Moluccas, swathes of Brazil, the Gold Coast — decade by decade, the Dutch stripped the Estado da Índia like creditors dismantling a bankrupt estate.

But nowhere were the consequences of the Iberian Union more poisonous than in Japan. The Tokugawa shogunate’s hostility toward Catholicism was, at root, a hostility toward what it perceived as a Spanish strategy of imperial conquest — send in the priests, convert the population, use the converts as a fifth column, then send in the soldiers. Whether this fear was justified is debatable. That it was sincerely held is not. And because Portugal and Spain now shared a monarch, the Japanese authorities held them jointly responsible for everything. When a Spanish galleon plundered a Japanese red-seal ship in 1628, the shogunate punished the Portuguese, reasoning — with impeccable legal logic, given the shared crown — that both nations were subjects of the same king. The fact that the Portuguese in Macau would cheerfully have sunk the offending Spanish galleon themselves was irrelevant.

The cascade of anti-Christian edicts, the persecution of converts, the expulsion of missionaries, the confinement of Portuguese traders to the tiny artificial island of Dejima, and finally the complete ban of 1639 — all of this is told in detail elsewhere on this site. What matters here is the end state: by 1640, Macau had lost the most lucrative trade route on earth. The annual Nau do Trato, Portugal’s great ship to Japan, no longer sailed. The silk-for-silver exchange that had sustained an entire city, funded the Jesuit missions across Asia, and connected Chinese manufacturers to Japanese consumers through Portuguese intermediaries — all of it was gone.

Macau was dying. And then, on 1 December 1640, a miracle happened — in Lisbon.

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Chapter Three

The Duke Who Became a King

The Portuguese Restoration of 1640 was one of those rare political events that genuinely changed everything. A group of conspirators stormed the royal palace in Lisbon, threw the Spanish governor’s secretary out of a window, and proclaimed the Duke of Bragança as King João IV of Portugal. The Spanish garrison, outnumbered and outmanoeuvred, capitulated within hours. After sixty years of captivity, Portugal was Portuguese again.

The new king had problems on a scale that might have discouraged a less determined man. Spain did not recognise the Restoration and was preparing to reconquer its wayward province. The treasury was empty. The army was threadbare. Half the overseas empire had been lost to the Dutch during the decades of Spanish neglect. João IV needed allies, he needed trade revenue, and he needed them immediately.

It was in this context — a newly independent kingdom scrambling for every diplomatic and commercial advantage it could find — that an adventurer named António Fialho Ferreira arrived in Lisbon in the autumn of 1643, carrying news that Macau had officially recognised the Bragança dynasty. Fialho Ferreira was a sea captain, a prominent Macau figure, and a man with a proposition: if the King would authorise a formal royal embassy to the Shogun of Japan, carrying credentials that announced Portugal’s separation from Spain, the Japanese might be persuaded to reopen trade. The argument, after all, was compelling. The shogunate’s primary grievance had been the Iberian Union itself. The Union was over. Portugal was now actively at war with Spain. Why would Japan continue to punish Lisbon for Madrid’s sins?

Fialho Ferreira was not alone in making this case. The Jesuit procurator Father António Francisco Cardim, a veteran missionary from Viana do Castelo with decades of experience in the East, had been lobbying the court with the same argument. The Leal Senado of Macau, the city council that had watched its economy collapse with the closure of the Japan trade, was desperate. Between Cardim’s ecclesiastical authority, Fialho Ferreira’s practical knowledge, and Macau’s economic agony, the pressure on the crown was overwhelming.

João IV authorised the embassy. It would be the first diplomatic mission to Japan carrying the direct authority of the Portuguese crown — all previous overtures had been dispatched by viceroys or regional governors. The King drafted a royal letter addressed to the “Emperor” of Japan, formally announcing the accession of the House of Bragança and laying out the case that an independent Portugal deserved a fresh hearing. Fialho Ferreira was rewarded for his initiative with commendas in the Order of Christ for himself and his eldest son Constantino, plus knighthoods for four of his other sons. He was appointed Captain-Major of the expedition’s two galleons.

The ambassador chosen to lead the mission was Gonçalo de Siqueira de Souza, an elderly fidalgo — impoverished but experienced, with a career that had taken him from the Spanish Philippines to the Persian Gulf. Siqueira was a man who understood the East, which was useful, and who was willing to undertake a voyage from which he might not return.

There was, however, a problem buried in the King’s instructions — a clause that would prove fatal to the entire enterprise. João IV strictly forbade his ambassador from offering any written guarantee that Portuguese Catholic missionaries would never again enter Japan. The King was prepared to separate his kingdom from Spain. He was not prepared to formally abandon the propagation of the faith. It was a principled stand. It was also, as events would demonstrate, the one thing the shogunate would accept nothing less than.

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Chapter Four

A Voyage of Spectacular Misfortune

The expedition departed Lisbon in January or February 1644, two galleons sailing for Macau via the Cape of Good Hope. What followed was a masterclass in everything that could go wrong on a seventeenth-century ocean crossing — and a few things that the most pessimistic sailing master could not have anticipated.

The original plan was straightforward: round the Cape, catch the monsoon winds across the Indian Ocean, and make directly for Macau. Instead, after rounding the Cape, the galleons veered too far south, missed the Java headlands entirely, and attempted to correct course toward the Coromandel Coast. The flagship São André fared worst. By the time she limped into the port of Anjer, near Bantam in the Dutch East Indies, on 6 November 1644, the ship was dismasted and over fifty of her crew were dead or dying. The consort vessel, meanwhile, had been separated by the same storms and forced to make for India alone.

And then the Dutch appeared. The authorities at Batavia — the nerve centre of the VOC’s Asian empire — towed the crippled São André into port and detained Ambassador Siqueira de Souza for four months. The Dutch were not at war with Portugal (technically), but they were certainly not going to expedite a Portuguese diplomatic mission to Japan, where their own hard-won monopoly as the sole European trading partner depended entirely on Portuguese absence. They held Siqueira just long enough to be inconvenient, then released him with a safe-conduct and the knowledge that the Dutch factory at Deshima had already warned the Japanese about the impending embassy — as early as 1643.

The São André finally reached Macau at the end of May 1645, battered but afloat. But now the expedition faced a logistical reckoning. One ship, badly damaged. No consort. An ambassador who had been detained by a hostile European power that had already tipped off the Japanese. The Macau city council, meeting in June 1645, made the sensible but agonising decision: they could not send a single weakened galleon to Japan alone. The São André would have to make the long detour south to Goa, beg the Viceroy for reinforcements, money, and men, and try again the following year.

It was on this Macau-to-Goa leg that the expedition suffered its most consequential loss. António Fialho Ferreira, the Captain-Major who had conceived the entire enterprise, lobbied the King, and carried Macau’s hopes across three oceans — died. The sources are sparse on the circumstances. He had apparently maintained lax discipline on the voyage and drawn sharp criticism from the authorities, but he was never formally tried; he simply died after reaching Goa in early 1646, somewhere between exhaustion and disgrace. His replacement was António Cabral, who was given command of a new flagship, the São João.

The Viceroy in Goa provided fresh men and supplies. The refitted fleet departed at the end of May 1646 and reached Macau on 27 July — only to discover they had missed the summer monsoon window for Japan. They set out anyway. A typhoon drove them back. The 1646 attempt was dead.

By this point, the embassy had been travelling for two and a half years. Its original captain was dead. Its original flagship had been replaced. It had been detained by the Dutch, battered by storms, diverted across the Indian Ocean and back, and thwarted by the weather. Any reasonable assessment of the situation would have suggested that the universe was trying to tell the Portuguese something.

They waited through the winter in Macau and tried again.

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Chapter Five

Fifty Thousand Men and a Pontoon Bridge

On 1 July 1647, two Portuguese galleons — the São João and her consort — departed Macau for the fifteen-day crossing to Nagasaki. They arrived on the morning of 16 July.

The Japanese were caught completely off guard. This was not supposed to happen. The Kyūshū coastal defences had been mobilised the previous summer, after the Dutch warned that a Portuguese embassy was coming, but when the 1646 attempt failed due to the typhoon, the authorities had stood down. Nobody expected the Portuguese to try a third time. The lookouts on the hills had to confirm what they were seeing: two well-armed European warships, flying colours that no ship had flown in these waters for eight years, calmly sailing into the bay as though the sakoku edicts were a suggestion rather than a death sentence.

What followed was a standoff that lasted nearly two months — a slow-motion confrontation between two powers operating from fundamentally irreconcilable positions.

The Japanese authorities did not immediately attack. The galleons were well-gunned, and a naval engagement would be costly. Instead, they opted for an approach that combined maximum intimidation with minimum violence: a blockade of overwhelming, almost theatrical force. Over the following weeks, the daimyō of the neighbouring fiefs mobilised their feudal levies and converged on Nagasaki. By mid-August, more than fifty thousand troops and two thousand watercraft of various sizes had been concentrated around the two Portuguese ships, which sat at anchor between the island of Iwojima and the entrance to Nagasaki harbour.

On the night of 14–15 August, the Japanese played their most dramatic card. Working through the darkness, they constructed an elaborate pontoon bridge — built from small boats lashed together — completely across the mouth of Nagasaki harbour. The galleons were sealed in. If Siqueira had harboured any thought of making a run for the open sea, he could now see, in physical timber and rope, the futility of the idea.

Ambassador Siqueira de Souza, to his credit, did not fold. He refused Japanese demands to surrender his ships’ rudders and ammunition — a demand that would have left him entirely at the mercy of a government that had decapitated the last Portuguese diplomats to arrive uninvited. As a gesture of diplomatic respect, he agreed to lower the ship flags bearing the Portuguese royal arms. But his guns stayed loaded and his rudders stayed mounted.

Negotiations — if that is the right word for a series of exchanges between an immovable shogunate and an immobilised ambassador — dragged on through August. Siqueira presented the case he had been sent to make. Portugal had a new king. The House of Bragança had nothing to do with Spain. The old Iberian Union was finished. The two nations were enemies now. Surely the shogunate could see the logic of reopening trade with an independent, anti-Spanish Portugal?

The shogunate could see the logic. The shogunate did not care.

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Chapter Six

The Clause That Killed the Deal

Towards the end of August, the answer arrived from Edo — a formal decree signed by all members of the Shogun’s great council, the Rōjū. Tokugawa Iemitsu, the third Shogun and the architect of the sakoku system, had considered Portugal’s argument and found it insufficient.

The decree acknowledged the change of dynasty. It recognised that Portugal was no longer under Spanish rule. It even conceded that Siqueira had arrived in good faith, unarmed with merchandise, simply to announce the accession of the new king. But none of this addressed the shogunate’s fundamental concern, which had never really been about Spain at all. The fear was Christianity — the faith that had converted hundreds of thousands of Japanese subjects, that had armed the rebels at Shimabara, that the Tokugawa believed functioned as the advance guard for European territorial conquest. And Siqueira’s credentials, for all their diplomatic polish, lacked the one thing the shogunate required: a specific, written guarantee that Catholic missionaries would never again set foot in Japan with Portuguese knowledge or assistance.

This was the clause João IV had forbidden his ambassador to concede. The King of Portugal could renounce Spain, but he could not renounce the Church. It was a decision rooted in genuine religious conviction, in the political reality that the Portuguese crown’s legitimacy was deeply intertwined with its role as a defender of the faith, and in the practical calculation that formally abandoning missionary activity in Japan would set a precedent for every other territory where Portugal’s presence depended on the Padroado — the papal mandate to spread Catholicism across Asia.

The shogunate’s rejection was, in its way, equally principled. Past experience had taught Iemitsu’s government that verbal promises from the Portuguese regarding missionaries were worthless. Priests had continued to enter Japan clandestinely for years after every ban. The only guarantee the bakufu would accept was an explicit, written, royal commitment — ink on paper, signed and sealed — that Christianity was finished as a Portuguese export to Japan. Anything less was a negotiating position, not a promise.

There was, however, one crucial mercy. Because Siqueira had arrived as a diplomatic envoy rather than as a trader violating the sakoku edicts — and because the shogunate had no desire to repeat the international embarrassment of the 1640 massacre, which had accomplished nothing except to make Portugal more desperate — the decree spared the lives of the embassy. The Portuguese would be allowed to leave.

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Chapter Seven

Through the Eye of the Needle

On 4 September 1647, the blockade was lifted. The Japanese had constructed a narrow passage at the eastern end of the pontoon bridge — just wide enough for the galleons to be towed through, one at a time, against the tide. It was a final performance of absolute control: the Portuguese would leave, but they would leave through a gap that the Japanese had built, at a pace the Japanese dictated, in a direction the Japanese chose.

The two ships were towed out of Nagasaki harbour and into open water. Behind them, fifty thousand soldiers stood down. The pontoon bridge was dismantled.

Eleven days later, the fleet reached Macau. By March or April 1648, it was back in Goa. In January 1649, the ships departed for Portugal. The news of Japan’s rejection took three years to reach Lisbon.

When it did, João IV capitulated. In 1651, a royal letter was drafted offering the most explicit assurances that no Catholic missionaries would ever again be permitted to leave for Japan with Portuguese connivance. It was a complete surrender on the one point the King had refused to concede four years earlier.

It was also completely irrelevant. The letter arrived far too late to change anything. And even if it had arrived in time — even if Siqueira had carried those exact words into Nagasaki harbour in the summer of 1647 — the sources suggest it would not have mattered.

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Chapter Eight

The Fears That Never Died

The decade following Siqueira’s departure confirmed everything the Tokugawa feared — and generated new terrors they had not yet imagined.

In the early 1650s, the shogunate uncovered a conspiracy among rōnin — masterless samurai, men who had lost their lords and their livelihoods in the great consolidations of the early Tokugawa period. These were not peasant rebels like the Christians at Shimabara. They were trained warriors, and the conspiracy aimed at nothing less than the overthrow of the bakufu itself. The shogunate’s long-standing anxiety that disaffected samurai might seek foreign backing — Catholic backing — suddenly looked less like paranoia and more like prescience.

Hard on the heels of the rōnin conspiracy came an even more alarming discovery. Between 1657 and 1658, the authorities in Kyūshū unearthed hundreds of kakure Kirishitan — hidden Christians who had been practising their faith in secret, without priests, without churches, without any contact with European Catholicism, for nearly two decades. The faith the shogunate believed it had extinguished was still alive, still spreading, still capable of binding Japanese subjects to a loyalty that superseded their loyalty to the state.

These twin shocks — armed conspirators who might ally with foreign powers, and a resilient underground faith that proved the Christian threat had not been eliminated — permanently hardened the bakufu’s resolve. Whatever slim possibility had existed that a sufficiently persuasive Portuguese ambassador, carrying sufficiently ironclad guarantees, might have talked his way back into Nagasaki, it died in the interrogation rooms of Kyūshū in the late 1650s. The sakoku policies would remain in force for the next two centuries, until Commodore Perry’s black ships forced the question in 1853.

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Chapter Nine

The Logic of the Gamble

It is tempting to see the 1647 embassy as an exercise in futility — a three-and-a-half-year voyage to hear “no” in person. But that reading misses the logic of the moment.

In 1643, when the embassy was conceived, the Bragança argument was genuinely novel. No one in Macau or Lisbon knew whether the shogunate would distinguish between an independent Portugal and the defunct Iberian composite state. The distinction was real, the strategic implications were significant, and the potential reward — the restoration of the most profitable single trade route in the Portuguese commercial empire — was enormous.

The failure was baked in at the level of instructions, not at the level of strategy. Had João IV authorised Siqueira to offer the written guarantee on missionaries — had the ambassador been able to pull that document from his dispatch case when the Rōjū’s decree arrived — the outcome might have been different. Not certain, but possible. The shogunate’s decision to spare the embassy’s lives suggests that at least some faction within the bakufu recognised the legitimacy of Portugal’s changed circumstances. The door was not open. But it was not locked from the inside.

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Sources & Further Reading

Boxer, C.R. The Great Ship from Amacon: Annals of Macao and the Old Japan Trade, 1555–1640. Centro de Estudos Históricos Ultramarinos, 1959. The definitive English-language account of the Macau-Nagasaki trade, including detailed treatment of the post-1639 diplomatic attempts.

Boxer, C.R. The Christian Century in Japan, 1549–1650. Carcanet Press, 1951. Essential background on the persecution of Christianity and the political dynamics that drove the sakoku edicts.

Boxer, C.R. Fidalgos in the Far East, 1550–1770. Oxford University Press, 1968. Covers the broader arc of the Portuguese presence in Asia, including the Restoration-era diplomatic initiatives.

Costa, João Paulo Oliveira e. O Japão e o Cristianismo no Século XVI: Ensaios de História Luso-Nipónica. Sociedade Histórica da Independência de Portugal, 1999. A key Portuguese-language study of the religious and diplomatic dimensions of the encounter.

Disney, A.R. A History of Portugal and the Portuguese Empire. 2 vols. Cambridge University Press, 2009. Comprehensive modern survey, with excellent coverage of the Bragança Restoration and its imperial consequences.

Elison, George. Deus Destroyed: The Image of Christianity in Early Modern Japan. Harvard University Press, 1973. The standard English-language study of anti-Christian ideology in Tokugawa Japan.

Lach, Donald F., and Edwin J. Van Kley. Asia in the Making of Europe. Vol. III. University of Chicago Press, 1993. Sweeping intellectual history that contextualises the Portuguese-Japanese encounter within broader European knowledge of Asia.

Massarella, Derek. A World Elsewhere: Europe’s Encounter with Japan in the Sixteenth and Seventeenth Centuries. Yale University Press, 1990. An indispensable synthesis of the full arc of European-Japanese contact.

Souza, George Bryan. The Survival of Empire: Portuguese Trade and Society in China and the South China Sea, 1630–1754. Cambridge University Press, 1986. Essential for understanding Macau’s economic crisis after the loss of the Japan trade.

Toby, Ronald P. State and Diplomacy in Early Modern Japan: Asia in the Development of the Tokugawa Bakufu. Princeton University Press, 1984. The revisionist study that reframed sakoku as controlled engagement rather than hermetic isolation — crucial for understanding why the shogunate’s rejection was strategic, not reflexive.

Valladares, Rafael. A Independência de Portugal: Guerra e Restauração, 1640–1668. A Esfera dos Livros, 2006. Detailed account of the Restoration and its diplomatic ramifications across the Portuguese empire.

Winius, George D., and Marcus P.M. Vink. The Merchant-Warrior Pacified: The VOC and Its Changing Political Economy in India. Oxford University Press, 1994. Useful for understanding the Dutch role in undermining Portuguese diplomacy in Asia.