In Pokémon Mystery Dungeon: Explorers of Time, Darkness and Sky, a Shiny Celebi is part of the main story, but is not recruitable. This same Shiny Celebi cameos in Pokémon Super Mystery Dungeon and can be rescued in an expedition, later connecting with the player.
In the Pokémon Mystery Dungeon WiiWare titles, 36 Shiny Pokémon can be encountered and recruited in dungeons, having a belly stat of 200 instead of 100. These Shiny Pokémon are,
- Caterpie
- Metapod
- Butterfree
- Tentacool
- Tentacruel
- Voltorb
- Electrode
- Magikarp
- Gyarados, which can also be obtained at Level 30 through a Wonder Mail password
- Hoothoot
- Noctowl
- Mareep
- Flaaffy
- Ampharos
- Hoppip
- Skiploom
- Jumpluff
- Wooper
- Quagsire
- Shuckle
- Slugma
- Magcargo
- Zigzagoon
- Linoone
- Wurmple
- Silcoon
- Beautifly
- Cascoon
- Dustox
- Roselia
- Barboach
- Whiscash
- Budew
- Roserade
- Skorupi
- Drapion
In Pokémon Mystery Dungeon: Gates to Infinity, a Shiny Ho-oh can be fought at Eternal Ruins through one of the Legend of the Mysterious Ruins job requests. It has a different moveset from the standard Ho-oh, but it cannot be recruited.
In Pokémon Mystery Dungeon: Rescue Team DX, 27 Mystery Dungeons will have strong foes spawn after first clearing them. These Pokémon have a chance to spawn shiny, but can only be recruited if the Friend Bow is equipped and their respective camps are purchased. These Pokemon include,
- Butterfree
- Ninetales
- Rapidash
- Electrode
- Exeggcute
- Exeggutor
- Starmie
- Magikarp
- Gyarados
- Ditto
- Dragonite
- Hoothoot
- Noctowl
- Ampharos
- Azumarill
- Sudowoodo
- Aipom
- Espeon
- Wobbuffet
- Shuckle
- Corsola
- Spinda
- Altaria
- Zangoose
- Metagross
- Ambipom
- Lickilicky
Additionally, Shiny Celebi returns in these games, being recruitable after clearing Purity Forest and visiting Mystery Houses.
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