Japan is a mostly Buddhist and Shintoist country with very few Christians. However, it does have a long history of Christianity that is little-known even in Japan. The story of the Hidden Christians in Japan is one of resilience, and survival. On our recent trip to the Goto Islands we went in search of the Hidden Christian sites in Japan that form part of the UNESCO World Heritage.
How Christianity came to Japan
At some point in the 16th century, Jesuit missionaries were quite successful in Japan. Many Japanese, particularly in Kyushu, converted to Christianity. However, the earliest Christians in Japan quickly faced persecution and suffered torture and martyrdom. Yet, many of the converts clung to their new faith and handed it down to their descendants. For centuries, these communities kept their religion alive in secret, even as the Tokugawa shogunate sought to eradicate Christianity from Japan. Over centuries of clandestine prayer meetings, the faith of the Hidden Christians took on a unique shape and quality.
Today, we can trace their footsteps through the Hidden Christian sites in the Nagasaki region and the remote Goto Islands, where many of them found refuge. Our journey takes us through museums, churches, and UNESCO World Heritage sites that tell the story of their endurance and the eventual rediscovery of their faith.
The Legacy of Christianity in Japan
Christianity first arrived in Japan in the 16th century with Portuguese traders and Jesuit missionaries. The religion quickly spread, particularly in Kyushu, and by the late 1500s, there were as many as 200,000 Japanese Christians. However, from the 1580s onward, the ruling authorities began persecuting Christians. Foreign priests were expelled or executed. The rulers forced Japanese believers to renounce their faith under the threat of torture and death.
By the 17th century, public Christian worship had disappeared, but some believers went underground. In remote villages, they formed communities of Hidden Christians (Kakure Kirishitan or Senpuku Kirishitan).
Sotome – The Origins of the Hidden Christians
Before heading out to the Goto Islands, we visit the Sotome region near Nagasaki, where many Hidden Christians once lived. Today, it is home to several museums and memorials dedicated to their history and the area is dotted with sturdy churches. Among the highlights is the Endo Shusaku Literary Museum, named after the author of Silence, which provides insights into the struggles of persecuted Christians.
At first thought, it is hard to imagine why the persecuted Hidden Christians would have built recognisable churches. But we quickly learn that none of the churches here date back to the period of persecution. Instead, they were only built in the 19th and 20th centuries, after the ban on Christianity was lifted. When European Christians arrived in Japan in the 1860s, some Hidden Christians recognised the similarities in their rituals and confided in the newcomers. With the newfound religious freedom, they started to build churches. Many eventually (re-) joined the Catholic Church.
During the Edo Period (1600–1868) and the persecution of Christians, however, the Hidden Christians kept their heads down and pretended to be Buddhists. But still, practicing the forbidden rituals at night held a risk of discovery and punishment. In search of greater safety, many Christian families eventually moved to the even more remote Goto Islands.
The Goto Islands – A Safe Haven for Hidden Christians
The Goto Islands, an isolated archipelago off the coast of Kyushu, provided a much better refuge for Hidden Christians during the Edo period. With rugged terrain and limited access, the islands were ideal for those seeking to avoid persecution. Then as now, the Goto Islands were sparsely populated, and the local governors looking for hardy settlers were often more willing to turn a blind eye to the religious activities of the Hidden Christians.
While not being able to practice their faith openly, the Hidden Christians found ways to meet in secret. The original Hidden Christian sites on the Goto Islands include meeting caves, graveyards, and wells where they would fetch holy water for baptisms. These locations offer a fascinating glimpse into the resilience of the Hidden Christian communities.
Today, the islands are also home to numerous churches and historical sites built after the end of persecution.
Fukue Island – The First Catholic Churches
Our exploration begins on Fukue Island, the main island of the Goto archipelago. While Fukue itself does not feature UNESCO-listed churches, it holds significant historical sites, including Dozaki Church. Built in 1877 – after the introduction of freedom of religion – as one of the first Catholic churches on the Goto Islands, it now serves as a museum.
Inside, we see relics from the period of Christian persecution. They include concealed prayer books and statues of the Buddhist deity Kannon, which Hidden Christians used to secretly venerate the Virgin Mary.
Hisaka Island – Japan’s Oldest Wooden Church
Next, we take a ferry to Hisaka Island, home to Dorin Church, one of the oldest wooden churches in Japan. Built in the 1870s by a local carpenter who had studied church architecture in Nagasaki, Dorin Church has a unique design. From the outside, it resembles a traditional Japanese house, while its interior features Western-style arches and stained glass.
The church is in a remote bay, where Hidden Christian families once lived in secrecy, evading government spies. The surrounding area is very quiet, and walking through the abandoned village near the church, we see remnants of terraced fields and stone houses. These settlements were once thriving communities, but after the legalization of Christianity in the 19th century, many families moved to larger towns, leaving the area to nature.
Narushima – A Community in Decline
Our journey to the hidden Christian sites in Japan continues to Narushima, an island with a deep yet fading Christian history. Here, we visit Egami Church, another UNESCO World Heritage site, known for its simple yet beautiful architecture. While the church continues to serve as a place of worship, its congregation has dramatically dwindled over the years.
On the day of our visit, preparations for a local shrine festival are underway, a reminder that Narushima’s cultural landscape is shaped by both Christian and traditional Japanese influences. Like many remote islands in Japan and comparably rural areas such as the Noto Peninsula, Narushima faces a steady population decline, with younger generations moving to the mainland in search of better opportunities.
Kamigoto – The Historical Heart of Hidden Christianity
Finally, we travel to Kamigoto, one of the largest islands in the Goto chain and a vital site for anyone exploring the Hidden Christian sites in Japan. Kamigoto has several well-preserved churches, including the striking Kashiragashima Church. Built entirely of stone, this church stands on a small island that had once served as a refuge for persecuted Christians during the Edo Period.
The Hidden Christians who settled here made a hazardous choice. They agreed to reclaim and work a rather barren, rocky land and to live among outcasts suffering from infectious diseases. All to avoid attention from the authorities! And so, this inhospitable environment became a sanctuary where their faith could survive in secret. Today, Kashiragashima church is a UNESCO World Heritage site. However, like many of the historic churches in the region, its congregation has dwindled to just a few members.
Reflections on our Hidden Christians’ Journey
Visiting the Hidden Christian sites in Japan, particularly in Nagasaki and the Goto Islands, provides a powerful glimpse into a remarkable chapter of Japan’s history. These resilient communities survived centuries of persecution, preserving their faith through secrecy and adaptation.
However, the declining populations on the islands highlight another challenge: preserving these historical sites in the face of modernization and migration.
For those interested in history, religion, or cultural heritage, the Hidden Christian sites in the Nagasaki region offer a profound and moving experience. Exploring these remote islands, we not only learn about Japan’s past but also witness a way of life that is slowly disappearing.
We are also very thankful and moved by the conversations we had with the people on the Goto Islands. Many of them were quite old and won’t be around much longer to tell their stories.
Reading recommendation
We enjoyed these two books about the Hidden Christians in Japan:
John Dougill: In Search of Japan`s Hidden Christians
We reread this travel account during our trip to Nagasaki and the Goto Islands. Being at the original locations added so much to the experience of reading it.
Shusaku Endo’s novel Silence tells the story of persecuted Christians in 17th-century Japan through the eyes of a Portuguese missionary. Based on real events, the book captures the hidden faith, suffering, and difficult choices faced by believers during the Edo period.
We enjoyed both the book and the movie by Martin Scorcese.
NB: We were not sponsored in any way to write this blog post and paid all expenses by ourselves. We may earn a commission for books bought through our links.
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