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It must be love.

Romantic and/or sexual relationships between characters (also called ships or pairings) 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.

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 Pairings

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". Pairings are organized by order of game appearance in each category.

Reimu and Marisa appear as playable main characters in almost every Touhou game, making this the most popular pairing in Touhou ever since the beginning. They are shown to be friendly in several places in the games, sharing a sort of on-again-off-again camaraderie. In the print works and art books, they are shown to spend nearly every minute with each other, from casually hanging out at the shrine and Kourindou to even solving incidents together. This is a rather popular pairing with fan authors, mostly displaying the contrast between Marisa's sassy, easygoing and spontaneous attitude, and Reimu's more unabashed, laid-back and level-headed demeanor.

Reimu Pairings

This relationship has origins on Story of Eastern Wonderland second stage conversation, where Reimu misinterprets that Meira is making a love confession.
Alice appeared to have remembered Reimu from their earlier encounters in Perfect Cherry Blossom and Mystic Square. This pairing was originally somewhat popular before IN's Magic team introduced the MariAli pairing.
Reimu and Sakuya both seem to work hard in their respective jobs.
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 fan works is usually identified by Yukari playfully teasing or flirting with Reimu, who often acts irritated or impatient with the advances but may become receptive to them eventually.
With no home to go to 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.
This pairing has gained quite a bit of popularity due to their partnership in Subterranean Animism. In Mountain of Faith, Aya also says "It's because I'm the one that knows the most about you." Knowing that Aya is always snapping pictures of everything, fans interpret that Aya snaps pictures of Reimu while she is alone.
It can be said that the pairing simply comes from the fact that the two are both shrine maidens, but the Mountain of Faith dialogues might bear some leads for it. It was the only popular pairing for Sanae before KogaSana came about.

Marisa Pairings

Marisa debuted in Story of Eastern Wonderland as the fifth-stage boss before Mima's final stage. She was consistently shown to respect Mima as a master or mentor figure throughout the PC-98 games.
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. Fan works in which they have a relationship vary greatly, with one of the most popular interpretations of MariAli being Alice acting like a typical tsundere toward Marisa, usually because Alice is a youkai and Marisa is not (bolstered by Marisa Stole The Precious Thing). Other times, Alice will be a less exaggerated tsundere, with strong feelings toward Marisa but unable to express them. In scenarios where they have a fully-blossomed, recognized relationship, the focus is centered on their contrasting personalities, as Marisa is extroverted while Alice is more of a calm, collected type.
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 fan works, Patchouli is often shown sharing her books reluctantly with Marisa in order to have a reason to spend more time with her. In many doujinshi and fanfics, she fights with Alice over who gets Marisa.
The first time they talked was stage 5 of Embodiment of Scarlet Devil, where Marisa expressed some desire to become a maid. A common depiction is that Marisa still sneaks around the library and is familiar with the Scarlet Devil Mansion residents, including Sakuya.
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 instead; actual Flandre x Reimu pairing is very uncommon, almost never seen.
This pairing probably originated from the notion that Marisa's trademark "Master Spark" was stolen from Yuuka.
This pairing was inspired by Nitori's interaction with Marisa as a selectable partner in Subterranean Animism.
Narumi and Marisa knew each other before the events of Hidden Star in Four Seasons, and are said to be on friendly terms.
Rinnosuke has known Marisa since she was a child, worked for her father, and created her mini-hakkero. The two are occasionally portrayed in fan works as harboring affections towards each other.

General Pairings

Yuuka is viewed as dangerous but gentle, while Alice has a somewhat contrasting personality.
The two share an unusual relationship as co-bosses in Mystic Square, in which the script diverges depending upon which boss the player defeats first. In the scenario where Mai is defeated, Yuki appears to care strongly about Mai, vowing to avenge her, while the traitorous Mai in the opposite scenario displays no concern at all. Fan interpretations of this dynamic can range from simple tsundere to angst.
As both are final bosses of PC-98 games, with one chasing the other in Mystic Square, this is a very common pairing.
It is alleged that Byakuren learned one of her spells from Shinki while she was sealed at Hokkai.
Both are youkai related to darkness, and Rumia has a spell card named "Night Bird".
The fact that they debuted on the same stage as fellow fairies has led fans to couple the two together.
Both are magicians who are shut-ins. As an alternative to common portrayals of each of them pining after Marisa, fans sometimes choose to pair the two together instead.
This pairing usually involves Meiling having an unrequited crush on Sakuya, and Sakuya frequently stabbing Meiling in the head for not doing her job as gatekeeper. However, the violent factor of this relationship has become less prevalent over time, for example with some fanart depicting a younger Sakuya looking up to Meiling like an older sister.
Both are handy at a particular ability, as maid and doll-maker, as well as having other kinds of similarities.
Both are secondary protagonist characters who share some similar traits. This pairing was popularized by Sougetsu-Tei.
Patchouli is a close enough friend to Remilia that the latter has allowed her to live in her mansion, possibly for centuries. In fact, as seen in Bohemian Archive in Japanese Red, they call each other by their abbreviated names, which suggests some level of intimacy.
The doll-maker and the living doll were seen talking during Remilia's party in Silent Sinner in Blue.
Besides both being two of the oldest residents of Gensokyo, in Perfect Cherry Blossom, Yukari is the one who informs the player that Yuyuko is the one buried under the Saigyou Ayakashi. This led to the popular fan theory that Yukari knew Yuyuko since before her death, and many doujinshi explore the relationship they had together, with quite a few suggesting that Yuyuko's suicide caused Yukari to fall into a deep depression.
This pairing results from the bonding together of oni companions who enjoy drinking and fighting.
Canonically, Tewi often plays practical jokes on Reisen or frames her so that Eirin can punish her. Reisen serves as the "straight man" counter to Tewi's trickster nature.
They are both fifth-stage bosses, and in Imperishable Night, Youmu concludes that Eirin is similar to Yuyuko in regards to treatment of their servants. There is also a contrasting nature of their weapons, where Youmu uses a sword and Reisen uses bullets.
Both characters from Imperishable Night are highly knowledgeable in their professions, and they are known for protecting the two immortals, Kaguya and Mokou, respectively.
Despite no canon connecting the two, this pairing was popularized by Mitsumoto Jouji's fancomic, Night Sparrow Love. Mystia is usually seen as admiring Mokou, who may or may not answer her feelings.
Keine appears in Imperishable Night's Extra stage to protect Mokou, when she said 「あの人間には指一本触れさせない!!」 or "You won't lay a single finger on that human!" Mokou confides in Keine in chapter four of Cage in Lunatic Runagate, citing her as one of the few people who understands her.
Bugs pollinate flowers, and Yuuka is a flower youkai. ANGELTYPE's depiction of this pairing (in Nightbug and Flowerland) features Yuuka acting as a protective big sister for Wriggle.
This is probably the most popular pairing featuring Medicine, either because of Medicine's alignment with lilies-of-the-valley or the fact the she is the only one to actually harm Yuuka when she is defeated in PoFV.
This pairing stems from the events following Cirno's Phantasmagoria of Flower View scenario.
The fanon interpretation of Momiji'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 harassment.
The origin of tengu is the god Sarutahiko, and the origin of miko is the goddess Ama-no-Uzume; according to mythology, these two were a married couple. As a result of this lineage, we have this pairing between the tengu Aya and the miko Sanae. Both have wind-based powers and are consecutive stage bosses in Mountain of Faith. This pairing may have been popularized by pasteltel.
Hina is the head of the Nagashi-bina doll army, and Medicine is a living doll, linking the two thematically.
As the goddess of misfortune and the unfortunate bridge princess, they both appeared in stage 2 of Double Spoiler.
This pairing is a prime example of the fandom trend of pairing bosses who debuted in consecutive stages. It is only a minor connection, but enough to make it one of the most popular ships for either character.
Momiji is known to play Dai-Shogi against kappa in her free time, and Nitori is the only kappa character introduced in the series so far.
This pairing often features the two acting as "parents" for Sanae. Despite Suwako losing her shrine to Kanako, the two seem to be on good terms.
As seen in Scarlet Weather Rhapsody, Iku acts as a guardian for Tenshi whenever she causes trouble.
After the events of Antimony of Common Flowers, Shion seems to have parted ways with Joon, now instead hanging out with Tenshi. As seen in Wild and Horned Hermit, Tenshi's natural good luck as a celestial seems to cancel out Shion's intrinsic misfortune. Because of this, she's one of the few people who can stand to be around her. Shion, who is used to being hated, strongly cherishes their relationship, and even the smallest acts of kindness from Tenshi will move her to tears. The two have been seen collecting ingredients for sake and have planned multiple banquets at the Hakurei Shrine together.
The two are thematically linked by the spread of disease and poison. In addition, they are also both depicted as outcasts.
Because the two are seen in the same location of Former Hell in Subterranean Animism, fans take their proximity as basis for probable interaction.
Yuugi has many traits for Parsee to envy, including strength, height, and fighting skill. As with Hina and Nitori, there is nothing actually to connect the two, yet the pairing turned popular enough to get lots of fan art and doujins, usually featuring Parsee as a typical tsundere and Yuugi as the more direct one.
Canonically, Orin triggered the events of Subterranean Animism because of concern over her friend Okuu. In doujinshi, the two pets are often seen to be affectionate with each other.
This pairing arose from the fact that their powers are polar opposites (fire and ice) and the fact that they are both portrayed as stupid. It also serves as the basis for the "cold fusion" pun, and ⑥⑨ (⑥ representing Utsuho and ⑨ Cirno).
Flandre and Koishi are both Extra stage bosses and both younger sisters. Some fans depict Koishi visiting Flandre to play with, seeking a relationship since their older sisters are too busy to pay attention to them.
This pairing became somewhat popular after Sanae's unusual interaction with Kogasa in the dialogue of UFO. It remains rather well-known thanks to works like Hitoshi Mizuki's Hang in There, Kogasa-san.
Both are underlings of rivaling religious factions. Aside from that, they also paired up in AoCF during the perfect possession incident.
They are co-workers on the Palanquin Ship, and they have also known each other for more than a thousand years. Reimu A's ending mentioned that both were sealed in the depths of the earth.
In canon, Nue mentions Minamitsu by name. Minamitsu's name also resembles that of the archer who supposedly sealed the mythological nue. The pairing seems to have spun from there.
Kogasa is the midboss of Nue's stage in Undefined Fantastic Object, although she has no relation to her or the plot. Due to the trend of pairing closely-placed bosses together, fanart of the two became common shortly after the game's release. Additionally, they are both youkai that enjoy scaring, or at least surprising, people.
In Symposium of Post-mysticism, Kyouko and Mystia are shown to be in a band together.
The historical counterpart of Yoshika, Miyako no Yoshika, wrote poems that were said to be liked by Ibaraki-douji, with Kasen even citing one of the poems in Wild and Horned Hermit. As a fellow hermit and Yoshika's owner, Seiga is sometimes paired alongside them as a threesome, or as Kasen's rival.
Both are hermits. Because of Kasen's straight-laced nature and Seiga's so-called wickedness, their relationship tends to be portrayed as abrasive.
Possibly based on the fact that Seiga was the one who introduced Miko to Taoism.
This pairing involves the penultimate stage boss and midboss of Ten Desires, as well as the two servants that Miko summons in one of her spell cards. Historically, the two have connections to rivaling clans.
Nue appeared in Mamizou's extra stage as her midboss. Mamizou was called in by Nue as a reinforcement. In her dialog, she mentions that her and Nue have been friends with each other for a long time. In Forbidden Scrollery, they are seen hanging out and conspiring to scare humans.
Kokoro considers Koishi her arch-nemesis after the two fought each other during the events of Hopeless Masquerade. They have relations to the keyword "heart," or "心," and are generally accepted to be both powerful and childlike. Due to the state of her third eye, Koishi is able to express emotions without restraint, while Kokoro cannot express emotions on her own.
The first- and third-stage bosses of Double Dealing Character, they were stated in their dialogue to be acquainted as part of the Grassroots Youkai Network. They share the similarities of both being more Occidental creatures (a mermaid and a werewolf) and both being rather mild-mannered compared to other youkai. This pairing was largely popularized in the western fandom by the artist Kagewaka.
Though lacking canon interaction, this pairing likely arose as a means to pair off the last member of the Grassroots Youkai Network after KageWaka. Sekibanki's species as a youkai is well-suited for scaring humans, juxtaposing with Kogasa's desire to be more scary, along with their contrasting personalities.
As there is not much connecting the two in canon, this pairing is seemingly mainly driven by their similar design, compatible aesthetic, and mischievous nature.
As the plot of Double Dealing Character revolved around Shinmyoumaru being tricked into working together with Seija, then confronting her about it in Impossible Spell Card, this pairing became a popular choice for dramatic or angsty fanworks. However, following Grimoire of Usami, they seem to have made up, leading fanworks to change their tone as well.
Both are amanojaku and have somewhat similar powers. In Grimoire of Usami, Seija got excited about her appearance, acting as if she was a celebrity.
Sumireko may have developed a crush on Mokou after her ending in Urban Legend in Limbo.
As consecutive stage bosses and fellow moon rabbits who deserted their positions together to remain on earth, they now run competing dango stands in Gensokyo and maintain a friendly rivalry.
Hecatia and Junko are canonically friends, and fan portrayals naturally extend this into romance. They are frequently depicted as parents to Clownpiece, as Hecatia treats the fairy with a free-rein motherly attitude in Visionary Fairies in Shrine, and because Junko's backstory centers on her grieving the loss of her son, this relationship offers her a new family dynamic.
The two appeared together as fifth-stage bosses in Hidden Star in Four Seasons and serve together as Okina's underlings.
The pair are stated to be friends in canon, with Momoyo in particular respecting Megumu's bravery when facing her. The pair are often shown together in ways that highlight their contrasting personalities, with Megumu being more refined and professional and Momoyo being gruff and casual.
Forbidden Scrollery establishes them to have been good friends since before the story started.
Kosuzu may have developed a crush on Mamizou after seeing her disguised as a human.
From her small appearance in CoLA, she's since come to hang around Kourindou. She often argues with Rinnosuke for the return of her stolen books, which are currently in his possession.
Being the only notable male character in the series, Rinnosuke often gets paired with characters for little reason other than as a self-insert for male fans. Some of the more notable pairings among them include Marisa, Tokiko, Yukari, and Sumireko.
As co-protagonists of the album stories set in a different time and place beyond Gensokyo's border, they are the only available pairing in their context and thus among the most popular ships in the series overall. Renko and Maribel are the sole two members of a night-activities club, and they share a strongly established partnership with trust and comfortable banter despite their contrasting ideologies. The two are known to frequent social locations like restaurants and bars in addition to their paranormal destinations, and in one album Maribel even travels to visit Renko's family. Their pairing is often referred to by the name of their club, the "Secret Sealing Club" (秘封倶楽部).

Rival Pairings

In a rivalry analogous to the sun and the moon, the two immortals canonically fight each other with deadly force, though they quickly regenerate all damage. In Inaba of the Moon and Inaba of the Earth, Mokou is shown to behave like a tsundere, while Kaguya genuinely likes Mokou. As a result, more works that explore the relationship nonviolently have been appearing, many portraying Mokou as a tsundere confused by her feelings. The idea that Mokou might redeem her family honor by wooing the princess who violated it has also been gaining ground. In Cage in Lunatic Runagate, Mokou expresses anxiety over the possibility of Kaguya returning to the moon. Related to this, another popular interpretation is that they find solace in each other as a way to cope with their mutual immortality. This solace is expressed in various forms — violence, friendship, romance — but despite the form by which they interact, they still desire to be around each other.
In Double Spoiler, Hatate appears as Aya's rival, running a competing newspaper with a contrasting approach toward journalism.
Yuuka is known for being a very strong youkai and for having painful battles, while Tenshi's role in Scarlet Weather Rhapsody was driven by her seeking the thrill of high-impact fights.
This pairing is fueled by their relationship in the official manga Wild and Horned Hermit and the unofficial manga "The Shinigami's Rowing Her Boat as Usual," both by Aya Azuma. As a hermit, Kasen must periodically fight off a shinigami like Komachi in order to extend her lifespan. As such, their interactions are mildly antagonistic, but Komachi treats the situation fairly casually and even offers her advice and information.
Cirno freezes frogs, and Suwako has thematic connections to frogs. This often causes them to fight, with Suwako winning most of the time.
Okina and Yukari are fellow sages, implying that they have known each other since before the creation of Gensokyo. However, they don't necessarily see eye to eye in their vision for Gensokyo, so they are sometimes depicted clashing. In Grimoire of Usami, Yukari's interactions with Okina can be interpreted as flirtatious.
The two religious/political leaders of Gensokyo, representing Buddhism and Taoism respectively, are often portrayed as being in conflict. However, since Hopeless Masquerade, there has also been a rise in fanart portraying them as having a more friendly rivalry or being the surrogate parents of Hata no Kokoro.
Sagume had ordered Doremy to create a duplicate Lunar Capital in the Dream World as a part of the former's plan. The two have been depicted as being friends or even lovers.
In Youmu's Otter ending of Wily Beast and Weakest Creature, Keiki expresses a desire to work together with the beasts again in the future, and Yachie states that she considers Keiki a worthy opponent.
Yachie gets along poorly with Saki but respects her strength.

Masters and Servants

The 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 fan works.

In the PC-98 games, Yumemi and her assistant Chiyuri share a dynamic similar to a manzai duo, with Yumemi as the "straight man" who punishes Chiyuri for foolish behavior. Fanon portrays Yumemi as being tsundere for Chiyuri.
In the PC-98 games, Yuuka is the owner and mistress of Mugenkan, and Elly and Kurumi are her subordinates. The fandom usually depicts Elly as Yuuka's caretaker.
As a god and the creator of Makai, it is speculated that she also created the people there, including Alice. Interpretation of this pairing can vary from platonic and motherly to romantic.
Koakuma is believed to be a demon, possibly a succubus, that Patchouli summoned and bound to serve her as an assistant librarian.
Many theories have been proposed to explain why Sakuya is so devoted in her service to Remilia, ranging from Sakuya being a defeated vampire hunter to other ways in which Remilia has manipulated fate.
This pairing can be depicted in several ways, most often seen with Meiling caring for Flandre in a motherly fashion, though portrayals can extend to romantic interpretations. Additionally, the two are seen as colorful characters, due to the nature of Meiling's rainbow-colored spell cards and Flandre's rainbow-colored wings.
Ran is often depicted as displaying either a motherly or a romantic 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 is more aware of surrounding events and often provides Youmu with expository explanations.
Ran is portrayed as the one who keeps the Yakumo household running, as Yukari is asleep most of the time.
In Legacy of Lunatic Kingdom, Hecatia tells Reisen that Junko has taken an interest in her, despite Junko being the self-proclaimed sworn enemy of Lunarians. Because Junko is unstable due to her past, fanworks often depict her as a stalker or otherwise one-sidedly clingy towards Reisen. In turn, depictions of Reisen can vary from being annoyed or creeped out to being fine with the attention. Although Junko is not Reisen's master, this pairing is listed under this category because it is often depicted similarly due to the difference in their power, age, status, and maturity.
Eirin's devotion to Kaguya is such that she is willing to do anything Kaguya asks of her, including violating the laws of the Moon to make her immortal.
Reisen's occupation as seen in her profile is "Kaguya's pet". The relationship is usually consensual, owing to Kaguya's gentle personality.
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. However, the relationship is also portrayed in a more consensual way as a medical assistant learning from a mentor.
In this case, Eiki is the serious boss, while Komachi is the flaky servant.
This was easy to predict, since Shou was the original helper of the sealed magician. Byakuren is depicted with Shou in a parent-like role (as she's shown toward every other boss in UFO) or sometimes a romantic one, following the trend of pairing bosses from consecutive stages.
Satori is shown to be very devoted to her pets, even when they get out of control sometimes.
Nazrin is Shou's underling and also the midboss in her stage. Similar to Ran and Chen, Shou's relationship with Nazrin is variously depicted as either motherly or romantic. However, unlike Ran and Chen, Nazrin is often portrayed with tsundere tendencies towards her higher-up.
In Ten Desires, she refers to Yoshika as "my cute underling." Some fanworks portray Seiga as having known Yoshika before her death and either being romantically involved or having a one-sided crush on her.
Tojiko serves Miko faithfully, appearing as a summon during Miko's boss battle, and her historical counterpart was one of Prince Shoutoku's consorts.
Futo is Miko's loyal subordinate, appearing as a summon during Miko's boss battle in Ten Desires and frequently praising the Crown Prince's strength throughout Hopeless Masquerade. In the past, she sided with Miko against her own Mononobe clan as she carried out their plan to become shikaisen together.
In addition to being the assigned leader of her army, Mayumi is an idol given life by Keiki, and she speaks of her with reverence.
As a Kurokoma, Saki is used to be the Prince Shotoku's horse (or as her theme depicts, the Pegasus).
As a daitengu, Megumu is settled above the other known tengus, taking a leader or boss place among them
Tsukasa presents herself as a loyal subordinate of Megumu, despite dealing behind her back at least once. Both are also seen with similar looking test tubes on their persons, with Tsukasa holding hers in her hand and Megumu wearing hers on her belt.
Hisami is depicted as having some kind of one-sided affection for Zanmu, The popularity of this depiction most likely comes from the dialogue of Hisami towards Zanmu in Unfinished Dream of All Living Ghost.

Sibling Pairings

The pair debuted together as the extra bosses of Lotus Land Story, with Mugetsu as the mid-boss and Gengetsu as Final Boss.
The two vampire sisters are individually among the most popular characters in the series, and fan works often choose to speculate further on their relationship. Flandre is portrayed as looking up to her older sister, and this complements Remilia's prideful nature.
Canonically, Satori expresses concern over her sister's condition, criticizing her decision to seal her third eye. Fan works often portray Koishi as trying to get Satori's attention, or Satori as one of the few who can sense her sister's presence.
The pair debuted together as the final bosses of Antinomy of Common Flowers, collaborating with their powers to cause an incident. Jo'on is shown to take advantage of her sister, but fans also portray her as having a soft side toward her.
Both are or were married. However, their husbands are never seen, bear little mention and have no major role in the story, only serving to establish the Watatsukis' relation to Eirin. Meanwhile, the sisters are often seen together and share a close bond.