The bosses are:

  • 1)Polluted Piranha Plant, huge Piranha Plants made out of sludge. Defeated by simply squirting water into their open mouths. They appear in Delfino Airstrip and Bianco Hills once, and three times in Delfino Plaza.
  • 2)Petey Piranha, who controls the Piranha Plants of Bianco Hills and appears in two of its episodes.
  • 3)Gooper Blooper, who controls the Bloopers of Ricco Harbor and appears in two of the harbor's episodes and one of Noki Bay's.
  • 4)Wiggler, who resides on Gelato Beach as the boss of the third mission, angry at Mario for disturbing his nap.
  • 5)Mecha Bowser, a giant mechanical version of Bowser, controlled by Bowser Jr. Appears only in the first episode of Pinna Park. (Mario must fight this boss while riding a roller coaster).
  • 6)Monty Mole, who shows up in two levels, both times arming a large, triple-gun cannon that fires Bullet Bills, Missile Bills, Bob-ombs, and Glorpedoes.
  • 7)Phantamanta, the silhouette of a giant manta ray appearing in Sirena Beach that splits into smaller manta rays when sprayed by F.L.U.D.D.
  • 8)King Boo, who commands Sirena Beach's Boos and only appears in Sirena Beach's Episode Five.
  • 9)Eely-Mouth, who has taken up residence under Noki Bay and is unwittingly poisoning the water with purple sludge.
  • 10)Shadow Mario/Bowser Jr., who, although causing the whole island's issues, never actually is the boss of a level, besides every level's one Shadow Mario chasing mission.
  • 11)Bowser, the final boss of the game, is found sitting in a hot tub full of green sludge floating in the skies of Corona Mountain. Bowser Jr. and Princess Peach are found with him.

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