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Kaguya-Mokou Inaba18 01

It must be love.

Romantic and/or sexual relationships between characters are an extremely popular subject in Touhou doujinshi and fanart. Of course, since almost all of the characters are female, "everybody in Gensokyo is gay" is itself a meme. Jokes aside, ZUN himself does acknowledge the idea of his characters getting romantically involved.

This is intended to be a list of the couples most commonly seen in fanon and excludes "crack pairings". Brief explanations of likely canon origins, or at least excuses, are also welcome.

Main Character Harems

As the protagonists, Reimu Hakurei and Marisa Kirisame are frequent subjects of shipping speculation, both with each other and with enemies they've defeated. Marisa, however, is often considered to have a larger "harem".

Reimu and Marisa appear as playable main characters, usually both in the same game, in almost every Touhou game. They are also shown to be acquainted in several places in the games, sharing a sort of on-again-off again camaraderie. This is a rather popular pairing with fan authors, mostly displaying the contrast between Marisa's sassy, easy-going and spontaneous attitude, and Reimu's more unabashed, laid-back and level-headed demeanor. Artists like Rocket Fuel 21 and Asian Big Brother Generation like to portray an affectionate and aggressive Reimu and a bashful Marisa (or Marisa crushing painfully on her in the second case), but those need to be taken into account as very personal interpretations those authors chose.
In one of the endings of Embodiment of Scarlet Devil, it is mentioned that Remilia often visits the Hakurei Shrine to have tea with Reimu. Naturally, this was taken further.
Reimu and Yukari — the border's shrine maiden and the youkai of the border — made up the Border Team of Imperishable Night. Their relationship in fanworks is usually identified by Yukari playfully teasing or flirting with Reimu (as Yukari does poke fun at her a lot in the game), who often acts irritated or impatient with the advances but may become receptive to them eventually.
With no home to go after the events of Immaterial and Missing Power, Suika was taken in at the Hakurei Shrine. It's plausible to think the oni can get very affectionate at times.
Could be said that it simply comes from the fact that the two are both shrine maidens, but the Mountain of Faith dialogues might bear some leads for it.
Alice appeared to have remembered Reimu from their earlier encounters in PCB, This pairing was originally somewhat popular before IN's Magic team introduced the Marisa/Alice pairing.
It's a pairing mostly based from the dialog between these two, however this can be Sanae too.
Sometimes referred to as "MariAli", mostly by Japanese fans, and "Malice" by English-speaking fans. Alice and Marisa make up the Magic Team of Imperishable Night, and as the two are both witches living in the same forest and have occasional quarrels, they are often shown to be friends. In fanworks the pair is depicted as being somewhat troubled, with Alice hiding her feelings for the often-oblivious(?) Marisa and getting exasperated by her attitude. Some works portray a "worst case scenario" in which the anxiety put upon her can become deadly, as she begins to develop obsessive and jealous tendencies that may end up in her harming Marisa or herself. This pairing is popular among fans, bolstered by the popularity of Marisa Stole The Precious Thing.
One of the endings to Embodiment of Scarlet Devil, plus articles from Perfect Memento in Strict Sense and Bohemian Archive in Japanese Red, all make reference to Marisa stealing books from Patchouli's library in the Scarlet Devil Mansion. It is assumed that there is a reason Patchouli tolerates this. In fanworks, Patchouli is often shown sharing her books reluctantly with Marisa in order to have a reason to spend more time with her.
Upon defeating Flandre in Embodiment of Scarlet Devil, Marisa suggests for Flandre to get married, with Reimu for example. At times fans will couple the young vampire with Marisa (actual Flandre x Reimu pairing is very uncommon, almost never seen), though. But the latter is still the one who gave her the hint.
Rinnosuke has known Marisa since she was a child, and the two are occasionally portrayed as harboring affections towards each other.
This pairing was inspired by the option of choosing Nitori as Marisa's youkai partner in Subterranean Animism's Marisa type C firing mode.
Koishi's profile in Subterranean Animism says she became attracted to the human who defeated her at the Moriya Shrine. Depending on which character you play as, this could be either Marisa or Reimu, but most fans prefer to pair Koishi with Marisa in order to keep Marisa's harem expanding.

Masters and Servants

The suffering and frustration experienced by serious-minded servants at the hands of their exasperating, capricious masters is a frequent source of humor in both official works (especially Inaba of the Moon and Inaba of the Earth) and fanworks.

Mima is considered to have been a mentor or motherly figure to Marisa during the PC-98 era.
Many theories have been proposed to explain why Sakuya is so devoted in her service to Remilia. Is she a defeated vampire hunter? Does Remilia feed on her blood? Is she just a lolicon?
Koakuma is believed to be a demon -- possibly a succubus -- that Patchouli summoned and bound to serve her as assistant librarian.
This pairing can be depicted in several ways, but most often seen with Meiling caring for Flandre in a motherly fashion, though fanon tends to take this further.
Ran is usually the only one keeping the Yakumo household running because Yukari is asleep most of the time.
Ran is often depicted alternatively displaying a motherly or a lolicon attitude towards Chen.
Youmu projects the image of a loyal samurai, but she's also a young girl who frequently gets flustered at Yuyuko's carefree personality. As seen in Silent Sinner in Blue, Yuyuko also has the best awareness of the plot and provides Youmu with expository explanations.
Eirin's devotion to Kaguya is such that she is willing to do anything Kaguya asked of her, including violating the laws of the Moon to make her immortal.
In their case, it's Sikieiki who's serious and and Komachi who's the flaky servant.
The fanon interpretation of Momizi's personality is very similar to Youmu's: serious about her duty as a guard and skilled with the sword, but innocent and naive in most other respects. This makes her a frequent target for Aya's teasing and abuse.
Kanako is dominant over Suwako, having taken control of Suwako's shrine by force, and Sanae is often depicted as being a level-headed shrine maiden who tries to keep both of her goddesses' antics under control.
The Komeiji sisters are shown to be very devoted to their pets, even when they get out of control sometimes. Canonically, Orin triggered the events of Subterranean Animism because of concern over her friend Okuu.
It's a PC-98 relationship between two humans, Yumemi being the older one, she often shows Chiyuri (Her assistant), a rather abusive side, which was taken further to the point of Yumemi, being tsundere for Chiyuri. In other words, a usual Master-Servant relationship, but in a more humane way.
Byakuren is considered the "granny" of the UFO team, and Nue and Murasa being the children of the team, so they would often fight for the one who likes Byakuren better. Often, things get messy between Nue and Minamitsu, sometimes turning into something more... seductive and flirtatious.
Nazrin is the underling of Shou, and also the midboss in her stage. Likewise to Ran and Chen, Shou is depicted as a motherly figure to Nazrin, or rather just romance.

General Pairings

Keine appears in Imperishable Night's Extra stage to protect Mokou.
Canonically, Tewi often plays practical jokes on Reisen, or frames her so that Eirin can punish her (see below under "Domination or Rape").
In Imperishable Night, Youmu concludes that Eirin is similar to Yuyuko in regards to treatment of their servants.
Patchouli is a close enough friend to Remilia that Remilia has allowed her to live in her house, probably for centuries. In fact, as seen in Bohemian Archive in Japanese Red, they call each other by their abbreviated names. This suggests some level of intimacy.
Comes from Cirno's ending in PoFV which features her and Aya.
In fanon, Cirno looks up to Letty as a motherly or big-sister figure whom Cirno can only see in winter, unlike Cirno who exists in Gensokyo year-round.
The doll maker and the living doll. They were seen talking during Remilia's party in Silent Sinner in Blue.
Yukari is a longtime friend of Yuyuko, having known her even before her death.
In Curiosities of Lotus Asia, Yukari is seen to visit Rinnosuke's shop, and they have a common interest in artifacts from the outside world.
Their stages are next to each other. It is only a minor connection, but enough to make it popular enough that it is almost the only pairing that features Hina.
The similarity of Nitori's hairstyle to that of PC-98 character Chiyuri led to jokes about them forming a "Twin-Tail Alliance". Their shared interest in science only furthered their pairing status.
Momizi is known to play Dai-Shogi against kappa in her free time, but Nitori is the only kappa character we know of so far.
The only two individuals known from the world past Gensokyo's border. In a night-activities club that consists of only them.
Often features the two acting as "parents" for Sanae.
Yuka is incredibly powerful, so it wouldn't make sense for her to pay attention to lower-level youkai. But Wriggle is a bug. Bugs pollinate flowers, and Yuka is a flower youkai. ANGELTYPE's depiction of this pairing (in Nightbug and Flowerland) features Yuka acting as protective big-sister for Wriggle, or alternatively showing her affection by tormenting her.
Spread of disease and spread of poison. In addition, they are also both depicted (in fanon) as outcasts, leading to a pairing.
Yuugi has many things for Parsee to become jealous over: strength, height, fighting skill, breast size.... As with Hina and Nitori, there is nothing to actually connect the two, yet the pairing turned popular enough to get lots of fan-art and few doujins. Usually features Parsee as a typical tsundere and Yuugi as the more aggressive one.
Another example of the trend in shipping consecutive low-level bosses.
Pairing that has been recently gaining popularity, despite no canon connecting the two. Usually has Mystia admiring Mokou, who may or may not answer her feelings. Supporters of this relationship will change Mokou's occupation to something other than a yakitori vendor, such as selling charcoal for Mystia's lamprey stand.
A relationship between the "intelligent" characters, based from one 4koma.
It was predicted, since Shou was the original helper of the sealed magician, Byakuren. She's depicted with Shou in a parent-like way(Among every other boss in UFO, and sometimes romantic. Being since their stages being right next to each other(Ultimate and Penultimate boss pairing).
It was not known why Kogasa protected the identity of Nue, even knowing she has no part of the main story's plot. Was it due to her being a close friend of Nue? Just from that theory, fans often show her with Nue, or even in an romantic way.
Both Flandre and Koishi were the younger sisters of Remilia and Satori and EX-Boss as well. A few fans suggest that Koishi is the one visiting Flandre to play with, or having a relationship since their older sisters are "busy" with their Servants.

Domination or Rape

As often seen, but may also be depicted in romantic and consensual contexts.

Usually involves Meiling having an unrequited crush on Sakuya, and Sakuya frequently stabbing Meiling in the head for not doing her job as door guard.
Similar to the previous pairing, but usually depicted with more extreme circumstances. Popularized by Sougetsu-Tei, after which "Fangirl Youmu" became a meme unto itself, with pictures of Youmu being photoshopped with a lovestruck expression wherever possible.
An extension of the meme about Yuyuko trying to eat Mystia.
Eirin is frequently shown, even in the canonical Inaba of the Moon and Inaba of the Earth, to subject Reisen to medical experiments and corporal punishment. As a side note regarding Kaguya, Reisen's occupation as seen in the profile is "Kaguya's pet".
Canonically, both of them continually fight each other with deadly force, even though they're immortal and regenerate all damage. In Inaba of the Moon and Inaba of the Earth, Mokou seems to behave like a tsundere as well, and Kaguya genuinely likes Mokou.
It's nearly same as the Yuyuko x Mystia pairing. Since Rin and Chen are cats, they're often depicted trying to catch the "mouse", which is Nazrin, and most of the time, teaming up.
Cirno freezes frogs, and Suwako has relations to frogs. This often causes then to fight with Suwako winning most of the time.
Reimu is always depicted wanting donations badly, so in order to get them, she uses Shou. Since Shou had the ability to attract treasures, Reimu forces her to bring money to her, but this always ends up in harassing Shou.
Yuka is known for being the strongest youkai, and for having painful battles. Tenshi is depicted as a masochist who keeps asking for punishment. You might notice what's happening here....
After Nue was defeated, Sanae asked her to come back with her to take a picture. Fans took this further making the SanaNue pairing. But, Nue does not want to be cared for by Sanae, as shown in this increasingly-popular 4koma comic.
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