- Wigglytuff: Wigglytuff is the guildmaster and sleeps in his own room to the right of the ladder that leads to he next floor. He is an important character throughout the story.
- Chatot: Chatot is Wigglytuff's assistant and best friend. He leads the team in morning cheers.
- Sunflora: Sunflora sleeps in the north crew room along with Chimecho, where her diary is found. She is the one who reveals the location of the Surrounded Sea to the player and partner. In the Special Episode "Today's "Oh My Gosh"," she can be played as the player Pokémon. Her quote is "Oh My Gosh!".
- Corphish: Corphish has no particular role in the game and sleeps in the south crew room along with Loudred and Bidoof and doesn't seem to notice Loudred's snoring. He tells the player how to take multiple jobs, like Snubbull in the previous games. His quote is "Hey, hey!".
- Loudred: Loudred is the 'alarm clock' of the Guild. He also supervises Diglett during sentry duty, but he is known to get angry if Diglett does not know the visitor. He has previously taken the Guild graduation exam...and failed miserably. He sleeps in the south crew room along with Bidoof and Corphish, and sometimes keeps Bidoof awake with his snoring. Before the player and their partner graduates, Loudred wakes them up each morning by shouting "UP AND AT 'EM! IT'S MORNING!". When he speaks some of the words he says are capitalized.
- Dugtrio: Dugtrio's role is to update the Outlaw Notice Board and the Job Bulletin Board. They wish to overcome their weakness of water and swim in the sea. This ends up in them being rescued by Team Raider. Dugtrio is the father of Diglett.
- Diglett: Diglett is usually the sentry, but the player is sometimes called to do sentry duty when Diglett is filling in for his father. The player can voluntarily do sentry duty after graduation. Diglett is Dugtrio's son.
- Croagunk: Croagunk runs the Croagunk Swap Shop, and is usually seen as creepy and weird. He apparently loves the stench that Skuntank gives off when Team Skull stays in the Guild. He also says that he could graduate at any time, but wishes to stay behind with his Swap Cauldron as he would become unable to stay and be with it. For some reason, he comes in and sleeps in the south crew room occasionally, but most of the time he stays with his Swap Cauldron. He begins most sentences with "Meh-heh-heh".
- Chimecho: Chimecho runs the Chimecho Assembly. She sleeps in the North Crew Room, along with Sunflora. She appears to be the chef of the Guild, making all the food and calling everyone for dinner.
- Bidoof: Bidoof sleeps in south crew room along with Loudred and Corphish. His diary is found there. He traveled with the player and their partner to the guild's expedition to find the treasure in Fogbound Lake. In the Special Episode "Bidoof's Wish," he can be played as the player Pokémon. His quote is "Yup Yup!".
- Team Skull
- Koffing: Koffing and Zubat steal the player's partner's Relic Fragment at the beginning of the game. Koffing and Zubat team up with Skuntank and join Wigglytuff's Guild but is later kicked out. In the Perfect Apple incident, he is knocked out by Koffing's and Skuntank's noxious-gas combo. His main quote is "Whoa-ho!".
- Zubat: Zubat and Koffing steal the player's partner's Relic Fragment at the beginning of the game. Koffing and Zubat team up with Skuntank and join Wigglytuff's Guild but is later kicked out. His main quote is "Heh-heh-heh".
- Skuntank: Skuntank is the leader of Team Skull. He teams up with Koffing and Zubat and joins Wigglytuff's Guild but is later kicked out. Skuntank is very cunning, for example, he eats all of the Perfect Apples in an attempt to make the player and their partner fail their mission and thus not be accepted into the guild's expedition. Skuntank and his team stole the player's partner's Relic Fragment a second time during the Brine Cave mission, but he eventually gave the item back after being defeated by Kabutops and the Omastar brothers. His main quote is "Chaw-haw-haw!".