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There are sixteen characters in this game. Seven characters from the previous Super Monkey Ball games return. There are nine new characters introduced in the game: Jet, C-AiAi, W-MeeMee, A-Baby, F-GonGon, P-YanYan, R-Doctor, N-Jam, and B-Jet.
- Monkey Island
- Aladdin's Castle
- Sweet Fountain
- Dragon's Journey
- Space Factory
- Mystic Dome
- Main article: Super Monkey Ball 3D/Stages
- Main article: Super Monkey Ball 3D/Glitches