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In Pokémon Super Mystery Dungeon, dungeons are mysterious places. they often have different layouts, different items, and different Pokémon. Each continent has a huge list of mystery dungeons. Here is the list so far.
| Dungeon | Number of Floors | Continent |
|---|---|---|
| Open Pass | 4 | Water Continent |
| Lush Forest | 5 | Water Continent |
| Foreboding Forest | 7 | Water Continent |
| Drilbur Coal Mine | 7 | Water Continent |
| School Forest | 8 | Water Continent |
| Glittering Mountain | 9 | Water Continent |
| Nectar Meadow | 9 | Water Continent |
| Poliwrath River | 9 | Water Continent |
| Ancient Barrow | 11 | Water Continent |
| Revalation Mountain | 13 | Water Continent |
| Sheer Mountain Range | 13 | Water Continent |
| Gentle Slope Cave | 7 | Water Continent |
| Mystical Forest | 9 | Air Continent |
| Fire island Volcano | 10 | Sea of Wonders |
| Showdown Mountain | 11 | Water Continent |
| Abyssal Badlands | 7 | Water Continent |
| Cave of the Deep | 7 | Water Continent |
| Calm Craggy Area | 7 | Water Continent |
| Reverse Mountain | 9 | Water Continent |
| Submerged Cave | 10 | Air Continent |
| Prehistoric Ruins | 9 | Ar Continent |
| Road to Primeval Forest | 9 | Sea of Wonders |
| Tree of Life: Roots | 7 | Sea of Wonders |
| Tree of Life: Trunk | 7 | Sea of Wonders |
| Sand Dune of Spirits | 10 | Sand Continent |
| Mystery Jungle | 30 | Grass Continent |
| Purifying Cave | 15 | Water Continent |
| Cave of Training | 6 | Water Continent |
| Leafy Highlands | 5 | Water Continent |
| Headwater Hollow | 10 | Water Continent |
| Longfield Cave | 6 | Water Continent |
| Sunbathed Garden | 7 | Water Continent |
| Serpentine Mountain Trail | 8 | Water Continent |
| Electric Wasteland | 10 | Water Continent |
| Waterfall Basin Grotto | 16 | Water Continent |
| Bustling Valley | 13 | Water Continent |
| Pledge Hill | 10 | Water Continent |
| Rolling Pass | 20 | Water Continent |
| Maze Meadow | 20 | Water Continent |
| Thrash Dungeon | 5 | Water Continent |
| Uprise Range | 4 | Water Continent |
| Stone Field | 5 | Water Continent |
| Odd Field | 6 | Water Continent |
| Peewee Meadow | 7 | Water Continent |
| Spring of Resolve | 28 | Air Continent |
| Rough Tunnel | 41 | Air Continent |
| Mysterious Plains | 8 | Air Continent |
| Small Sand Dune | 10 | Air Continent |
| Berry Forest | 12 | Air Continent |
| Super Apple Forest | 16 | Air Continent |
| Elegant Gorge | 10 | Air Continent |
| Moonlit Cave | 10 | Air Continent |
| Frosty Tree Steps | 10 | Air Continent |
| World Tree | 18 | Air Continent |
| Ghost Island | 22 | Air Continent |
| Red Point | 10 | Air Continent |
| Yellow Point | 10 | Air Continent |
| Distress Mountain | 22 | Air Continent |
| Forest of Bounty | 5 | Air Continent |
| Thorny Shadow Path | 15 | Grass Continent |
| Deep Ocean Tunnel | 25 | Grass Continent |
| Temple Remains | 39 | Grass Continent |
| Sacred Ruins | 39 | Grass Continent |
| Hidden Cave | 30 | Grass Continent |
| Heart Lake | 29 | Grass Continent |
| Path of Fallen Leaves | 42 | Grass Continent |
| Sunny Spot Hill | 10 | Grass Continent |
| Friendly Meadow | 12 | Grass Continent |
| Abundant Pass | 14 | Grass Continent |
| Stealth Cavern | 16 | Grass Continent |
| Crystalline Maze | 18 | Grass Continent |
| Little Canyon | 13 | Grass Continent |
| Spiral Vortex | 16 | Grass Continent |
| Giant Stone Meadow | 15 | Grass Continent |
| Fresh Meadow | 15 | Grass Continent |
| Blue Point | 10 | Grass Continent |
| Triangle Temple | 12 | Grass Continent |
| Sky Ruins | 1 | Grass Continent |
| Dragon Gate | 23 | Grass Continent |
| Magma Chamber | 27 | Grass Continent |
| Zero Isle | 13 | Grass Continent |
| Freedom Coast | 5 | Grass Continent |
| Lake of Enlightenment | 30 | Mist Continent |
| Aurora's Edge | 43 | Mist Continent |
| Midnight Sun Gorge | 9 | Mist Continent |
| Forest of Fairies | 11 | Mist Continent |
| Flagstone Cave | 13 | Mist Continent |
| Frozen Mountain | 15 | Mist Continent |
| Pumpkaboo Forest | 19 | Mist Continent |
| Frozen Falls | 17 | Mist Continent |
| Gooey Bog | 13 | Mist Continent |
| Buried Ruins | 20 | Mist Continent |
| Clear Lake | 18 | Mist Continent |
| Island of Isolation | 1 | Mist Continent |
| Meteorite Crater | 8 | Mist Continent |
| Cape of Wonders | 9 | Mist Continent |
| Apex Mountain | 31 | Sand Continent |
| Stone Tree Mountain | 44 | Sand Continent |
| Yellow Sand Labrynth | 10 | Sand Continent |
| Valley of Strong Winds | 11 | Sand Continent |
| Hall of Magic | 12 | Sand Continent |
| Thirsty Desert | 13 | Sand Continent |
| Secret Quarry | 18 | Sand Continent |
| Holey Meadow | 15 | Sand Continent |
| Snowy Cave | 17 | Sand Continent |
| Sandy Cave | 12 | Sand Continent |
| Jewel Road | 13 | Sand Continent |
| Fossil Excavation | 15 | Sand Continent |
| Isle of Light | 15 | Sand Continent |
| Mysterious Geoglyph | 8 | Sand Continent |
| Golden Suite | 11 | Sand Continent |