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Main installments:
Danganronpa: Trigger Happy Havoc
- Kiyotaka/Mukuro is a ship that has grown in popularity, primarily among the Japanese fanbase. They didn't interact much during the one chapter they had together in which Mukuro was disguised as Junko, and didn't have any established connection with one another. Not to mention, Mukuro is all but stated to have feelings for Makoto. The most likely explanation for why may be due to their specific talents.
- Sayaka/Mukuro, despite almost never interacting outside of some minor bonus material and both of them dying in the 1st chapter, have a surprising amount of fanfiction and art dedicated to pairing them up as well. On Archive of Our Own, it's even Sayaka's most popular pairing, while on Mukuro's side it's the second-most popular one.
- Leon/Yasuhiro also seems to be fairly popular, despite the two of them hardly having any interaction at all. This seems to be based on the fact that Leon used Yasuhiro's crystal ball as a throwing weapon in both the original game and IF.
Danganronpa 2: Goodbye Despair
- Nagito/Mikan has a surprisingly large group of fans for a ship where the two characters barely interact.
Spin-offs:
Danganronpa Another Episode: Ultra Despair Girls
- Takemichi (Mondo's captive) and Yuta have grown into a surprisingly popular ship, despite neither character interacting, Yuta dying before having much Character Development, and Takemichi not appearing in the game at all.
Other:
Across Multiple Installments
- Kiyotaka is often paired with Peko, despite her canon interest in Fuyuhiko, and the fact that she and Kiyotaka don't even interact during V3's Talent Development Plan. This is because of their shared interest in Kendo. This is helped by official artwork of them practicing together
◊. - It's not unheard of to ship Leon with Ibuki, mainly because Leon both admires and wants to be a punk musician and Ibuki is a Fun Personified version of one- they even get to interact in the Danganronpa V3: Killing Harmony Bonus Mode, which only gives the ship more material.
- Thanks to a very cute interaction in Danganronpa V3: Killing Harmony's Bonus Mode, Mondo/Mikan has some supporters too, which is surprisingly cute and plays off each other well, with Mikan chasing after Mondo to bandage his injuries and Mondo going along with it, despite being used to injuries like that, so that Mikan won't be sad..
- Despite Fuyuhiko's interest in Peko, he and Chihiro ended up having a couple shippers thanks to them having insecurities over their small figure and not looking very masculine.
- Despite both characters'... reputations among the fanbase, it's not unheard of for people to ship Hifumi Yamada with Tsumugi Shirogane. Almost certainly because of their shared status as proud Otakus.
