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Christianity is rare enough in Japan that a character being explicitly labeled as such is rather unusual.
This was not always the case. When trade between the West and Japan was largely conducted though Jesuit priests, there was a pretty substantial Christian base. From the time the first Jesuit started a mission in 1548 to just 40 years later in 1589, there were about 200,000 Japanese converts, becoming the largest overseas Christian community (yes, even more than Mexico and South America, which had a substantially higher monetary investment, and head start) and was unique in that it was largely run and evangelized by Japanese. This was largely because Shinto tradition permits worshipers to openly practice multiple faiths. Buddhism, for instance, arrived earlier and was quickly integrated into Shintoism. Today, many temples exist next to shrines, and many Japanese practice both Shinto and Buddhist rituals.
Christianity, however, was increasingly seen as a threat to the existing social order.
Christians were harshly persecuted during the Tokugawa era (early 1600s) and driven underground out of fear that Japanese peasants and samurai would feel more loyal to a foreign Pope than their own lord. This was exacerbated by the Protestant Dutch, who hoped to undermine their trade rivals by spreading rumors of Portugal's previous conquests. The fact that the King of Portugal actually asked the priests about the feasibility of an invasion of Japan probably didn't help. Neither did their numerous military activities and destruction of Shinto Shrines and Buddhist Temples. What followed was a bloodbath, with all priests (Portugese or otherwise) being expelled or crucified (and yes, they did do that on purpose). Converts were hunted (one practice being that soldiers would go to villages and demand they stomp on a picture of Jesus or Mary, any which showed hesitation were branded Christians) and sent to Nagasaki to be tortured. If they refused to recant, they were also crucified.
The surviving underground religion became greatly influenced by Buddhism, Taoism, and Shinto.
In modern days with the advent of globalization and the reopening of Japan, its no surprise that most major Christian sects have a presence (if small) in Japan.
- Anime Catholicism
- Christmas in Japan — Almost always secular (except when this trope comes into play), and with some different traditions.
- One of which is that Christmas is considered a couple's holiday, the family holiday being New Years.
- Christianity Is Catholic — Since Roman Catholicism was the only denomination to ever seriously take root in Japan, it makes sense that most of their portrayals of Christianity as a whole would be influenced to some degree by Roman Catholic practice.
- Church Militant — These get their own page, so don't list them here unless they have something more to contribute.
- Nuns Are Mikos
- Faux Symbolism — Christian symbols simply being used for their exotic factor, much like Eastern religious symbols being used in the West for that purpose.
- Creepy Cool Crosses are just worn or depicted because they're cool... or because they're supernatural, or both.
- Weddings in Japan — Conspicuous by being done in the Christian style. Whatever religion they follow, most Japanese aren't strict enough to mind doing another faith's tradition, and Christian weddings are comparably inexpensive and pretty.
- The usual adage about the Japanese's tendency to mash up religious practices is: "born Shinto, marry Christian, die Buddhist".
- Sakamichi no Apollon is interestingly accurate in it's portrayal of Christians. Both Sentaro and Ritsuko are explicitly shown as practicing Christians, probably Catholic, and they are seen in church together, Ritsuko with her head covered, while singing the hymn "Jesus Paid It All" in Japanese. Sentaro wears a cross around his neck and Ritsuko has rosary beads but doesn't carry them around with her.
- Much of Shogun discusses this trope in great detail, with the Protestant protagonist out to destroy Jesuit influence in feudal Japan.
- If some comments and actions by Brock and Misty in Pokémon Shipwreck and The Ghost of Maiden's Peak are of any indication, those two are apparently of this trope (as the former explicitly referenced the Bible story about Noah's Ark, and the latter attempted to use, among other things, a Crucifix to ward off a Gastly).
- To Aru Majutsu no Index: Kaori uses how Christianity in Japan had to go underground and blend with the dominant religions in Japan as justification for why she (a Christian) is able to fight an archangel.
- One of the stories in the Lone Wolf and Cub manga deals with the persecution and martyrdom of Christians during the Tokugawa era.
- The Ghost in The Tokaido Inn deals with underground Christians a lot.
- Know Your Enemy Japan gives an overview of how the Bushido warlords reacted to Christian missioniaries and emerging Christian churches in Japan.
- In Rurouni Kenshin, one of Kenshin Himura's strongest opponents was Shougo Mutou aka Amakusa, a Christian Religious Bruiser trying to end the persecution of his fellow believers by helping a "holy man" overthrow the Japanese government, and basically an Expy of real life Christian leader Shiro Amakusa. Kenshin essentially ended up fighting Samurai Jesus. And winning.
- Not only that, but Shougo and his younger sister Sayo were the leaders of a small Japanese Christian colony hiding in Shimabara, a rural area near to Nagasaki. And several years before, they barely managed to survive a major massacre in the same Shimabara area, in which their parents and everyone in their Doomed Hometown were killed for their beliefs.
- In the manga Midnight Secretary Japanese vampires are specifically said to be weak against the piety of Christians. Luckily for him Japan is pretty secular, even on Christmas, but at one point Kyouhei is at a business dinner held by a Japanese family who were devout Christians and it made Kyouhei very sick.
- Lucky Star has some Mikos who also sing in a Christian choir and play "Joy to the World" on their recorders. Their comment is that they pray to all gods. (Shinto is about animism. Why not!) Although they wonder whether it's all right for one of their collegues to marry in a Western wedding dress.
- The Messian Church (or you can spell it Mesian, whatever) in Shin Megami Tensei I is the "endtimes-crazy" type of Christian flanderized to such an extreme that they are willing to launch nukes to bring about their "Thousand Year Kingdom". Though the one that did said action was American (or claimed to be), the majority of Messians you encounter are Japanese.
- They represent the Law Faction - the one representing archetypes as justice, charity, and unity. Also, brainwashing, totalitarianism, and intolerance. The other side's not so hot, either. Crapsack World, gentlemen.
- The hero of Tales of the Otori grew up in a hidden Christian village (which gets destroyed at the beginning of the first book).
- Gabriel Goto of Neal Stephenson's The Baroque Cycle is a Catholic Ronin in a rare example by a non-Japanese author.
- Maria Holic has a lot of fun with the whole Lesbian Catholic Schoolgirls genre, but in a rare serious moment has the Student Council President explaining that most of the students aren't Christian, the nuns aren't forcing anyone to their beliefs, and how one can appreciate the values without sharing the core beliefs.
- A fairly surprising amount of fanon in the Ranma ½ fanfic community grew from one single (non-story) image of Kasumi Tendo wearing a cross on a chain. However this probably reflects nothing more than Takahashi's habit of creating promotional images depicting her characters wearing whatever happened to be fashionable at the time.
- In Twentieth Century Boys, Father Nitani helps out La Résistance from his church in Kabuki. He's also a close personal friend of The Pope.
- In the Nasuverse, the original founder of the Tousaka clan was a Christian, thus justifying his descendants' (Rin in Fate/stay night and her father Tokiomi in Fate/Zero) close relationship with the local church.
Shiki: "Chris-chan? What's with that question, all of a sudden? I don't know any girl who's got a name like that."
- At the start of Tokyo Godfathers, Gin and Hana attend a Christian church service just so they can get a free handout of some food.
- Hana at least seems to actually be a believer, to some degree, at least enough so that she muses about how, if God could impregnate a virgin woman, He could almost certainly get a transgender lady such as herself with child.
- In Wandering Son, Saori Chiba converts to Christianity. Whether she does this out of true conviction or out of some misplaced feeling of guilt is not quite clear. In any case, she's not very diligent in attending Church.
- She met a boy, Fumiya, at Church. He seems rather casual about being Christian though, even smoking in church (he seemed around eleven to thirteen too).
- In Ouran High School Host Club a few characters are seen wearing crosses (in the manga, anyway). While it's doubtful they are Christian, there's a possibility that Tamaki is. He was born and raised in France until he was fourteen before being shipped off to Japan. Chances are his mother is Christian, but it's not really relevant to the story and therefore never brought up.
- In Weiss Kreuz, Ken was Raised Catholic, even spending a period of time in a Church orphanage, and it shows. In later canon, Aya also shows interest in the faith - it's arguable whether or not he actually practices it, and in any case he doesn't hold with its doctrine of forgiveness, but a conversation with a nun in Fight Fire With Fire reveals that he's worn out a Bible reading it every night before he sleeps.
- It appears that most of the Maria-sama Ga Miteru cast are Catholic.
- The subject of the actual faith of the characters is only brought up a few times, surprisingly. One character ( Shiori) wants to become a nun, and another is revealed to be both Christian and belongs to a Buddhist family (Shimako). It's mentioned outright at one point that one does not have to be a Christian to attend Lillian.
- On a serious/literary note, there have been several important Japanese Christian writers, of whom the most important is probably Endo Shusaku. He wrote several novels about many subjects, but the most famous is Silence (Chinmoku in Japanese) about a 17th-century Portuguese missionary in Japan who has to shepherd his flock through the initial Tokugawa persecution. Said novel was adapted into a film by Martin Scorsese, with Andrew Garfield and Liam Neeson as the protagonists.
- He also wrote numerous short stories and various other novels on the topic, including A Life of Jesus. And, of course, Deep River, a.k.a. Japanese Christianity: The Book. It served as a very personal account of what it means to be a Christian in a country that's 99% atheist/Buddhist/Shinto and extremely suspicious of outside influences.
- Superbook is about a Japanese family who travel to important Biblical moments.
- In Mai-HiME, Fuka Academy has its own small church, staffed by a priest with a Western name and a Japanese nun. Like just about everything about the school, both are not what they seem.
- In Puella Magi Madoka Magica, the character Kyouko Sakura is one, given that her father was a preacher. (Likely a Protestant minister, for obvious reasons.) On the other hand she no longer seems to be practicing the religion in any fashion. It's appropriate, since the story has numerous references to Faust...and Kyouko made a Deal with the Devil that went very wrong. and finished in a Pater Familicide. Even more so, Gen Urobuchi has apparently said that had Kyouko not taken said Deal with the Devil, she would've returned to the ruins of her home and rebuild them into an Orphanage of Love.
- Additionally, the witch Elsa Maria has a bit of Christian symbolism to her. She was likely to have been a Japanese Christian when she was human.. Some fans speculate that she either was Kyoko's Dead Little Sister or a membress of Kyoko's father's cult.
- Homura mentioned having gone to a Catholic school prior to transferring.
- Meta-example: Manga creator Yamahana Noriyuki is a proud Christian. He tends to discuss his faith in the author's notes at the end of his manga volumes. In this (excellent) series, Orange Yane no Chiisana Ie , the scanlators were kind enough to translate these notes. Also, the maternal grandmother of the girls imparts Christian lessons to the children from time to time. Yamahana's faith does not prevent him from indulging in Fan Service, though; he's still a manga-ka, after all.
- Award winning author Ayako Miura wrote several books that elaborate on her trip from Nihilism to Protestantism as well as several novels that have several Christian themes such as "Shiokari Pass" and the better-known "Hyoten", the latter being adapted as a television drama series
- The Feudal-era secret Christians who heroically sacrificed their lives for a single crucifix in Usagi Yojimbo.
- The persecution of Christians is part of the background in Samurai Champloo, which is touched upon in the episode showing the Dutch East India Company as well as one revolving around a supposed descendent of Francis Xavier, who manipulates Japanese Christians. Japanese Christians ultimately are part of a reveal at the end of the series namely that Fuu's Disappeared Dad (the "Samurai who smells from Sunflowers") was one, and he left the family to not involve them in the persecutions.
- Another meta example: Yasuhiro Nightow, creator of Trigun, is a Christian convert, and lots of intentional symbolism can be found in his work (Nicholas Wolfwood, anyone?).
- Karen Kasumi of X 1999 is a Japanese Christian. Her mother converted both of them to it, though it seems that it was only to hide from cults who wanted to use Karen's fire powers for their own ends.
- The Dresden Files has an interesting example in Knight of the Cross Shiro, who was born and raised in Japan, and was accidentally baptised while attending an Elvis Presley concert (some Baptists in the audience asked if he wanted to meet "The King," and Shiro's faulty-at-the-time grasp of English made him think they meant Elvis). Even though his conversion was by accident, he made an effort to be as good a Christian as he could.
- Considering he was good enough (both in the moral/ethical sense and the skill sense of the word) to become a Knight of the Cross and stay one long enough to grow old, it's safe to say he succeeded.
- After the Quake. All god's children can dance. Yoshiyo is a Japanese Christian (this is why he told his girlfriend that he couldn't marry her; that he was a son of god and couldn't ever marry). His mentor and his mother, as well.
- In Yami no Matsuei, we're introduced to Muraki in Nagasaki's famous Oura Catholic church (which Tsuzuki ran into while chasing a vampire). Later, while dragging Tsuzuki around town after kidnapping Tsuzuki's partner, Hisoka, Muraki mentions ways the persecuted Japanese Christians would disguise their worship (i.e using statues of Kannon to represent the Virgin Mary). This has lead to the idea of Muraki being Raised Catholic becoming minor fanon.
- Miu Sakurai and Shion Amamiya from Akuma na Eros attend a Catholic school and are Japanese Christians. The manga starts with Miu praying in the school chapel, and then Amamiya walks in and talks to her. There's a major subversion, though: Amamiya is actually an angel under the disguise of a Christian boy.
- Love Exposure focuses on a very Dysfunctional Family of Japanese Christians.
- The first zombie we see getting killed by Z-Loan is a nun at the school that Shito, Chika and Michiru attend, and they all wear crosses somewhere on their uniforms.
- The main character (played by Japanese av model Sora Aoi) of Big Tits Zombie is heavily implied to be a Christian. She prays to "the Lord" a few times, crosses herself while standing over the body of one of her friends, and when it came time to make a grave for said friend, she placed a cross over it. She lived in Mexico for a number of years, which could be the explanation.
- Welcome to The NHK: Misaki's aunt is one and forces Misaki to attend church groups as a condition of taking her in.
- Saya's teacher in the animated movie Blood: The Last Vampire is a Christian and wears a cross necklace, which pisses off Saya because crosses and references to Jesus are either her weakness or they draw in the bigger, more beastly-looking vampires she's trying to fight.
- Himeko and Chihiro from Narcissu ~Side 2nd~ are Catholic, though the former has lapsed while the latter is very devout. Much of the story concerns Himeko's struggle to resolve her crisis of faith before she dies.
- Zakuro Fujiwara from Tokyo Mew Mew is a practicing Christian in the original anime, going to church regularly and using a cross as the handle for her Weapon of Choice. (Unusually for a Japanese Christian, she appears to be a Protestant.) This was Bowdlerised in the dub; all crosses were changed to sticks without sides, leading to the fandom joke that Renee venerates toothpicks.
- Real Life example: seiyuu Kuwata Kong [who is known to voice characters in the SNK franchise - more prominently Geese Howard - as well as Large Ham Kikuchiyo from Samurai 7], is a Japanese Christian [his profile from Anime News Network list him also as a 'gospel singer].
- Goto Dengo converts to Christianity near the end of Cryptonomicon.
- Between 1885 and the start of 2012, there have been 58 unique Prime Ministers of Japan. Seven were Christians (three Catholic, four Protestant), a disproportionately high ratio compared to Japan's general population.
- In Michiyo Akaishi's Amakusa 1637, Action Girl Natsuki Hayami, her boyfriend Masaki Miyamoto and their friends are students from a Catholic school who get Trapped in the Past... and arrive to the Nagasaki of few before the tragic rebellion by Shiro Amakusa. Natsuki, being Amakusa's genderflipped Identical Stranger, sets out alongside her friends to change history and avert the massacre. They sort-of succeed.
- In Total War: Shogun 2, Christianity might play a serious role in the game. Being a Japanese Christian clan means you can access European guns and cannons, plus your Christian citizens will put up serious resistance against non-Christian clans who occupy their cities. Of course, since embracing Christianity means the rest of Japan will hate you, it's best taken by clans which are not based on the main island.
- Real Life Example: Seiyuu Toshio Furukawa, voice of Piccolo in Dragon Ball and Kai Shiden in Mobile Suit Gundam, is a practicing Christian.
- Real Life Example: Eiji Tsuburaya, creator of Ultraman and partly of Godzilla, was a Catholic, as are the Tsuburaya family since then.