Dungeons are located underground. The locations of the entrances are randomized each game; however, they are always found below the Rock layer. When an entrance is nearby, the background tiles will be black, sometimes with carved symbols.
List of all the caves and dungeons -
| Name | Information | Location |
|---|---|---|
| Fire Cave | The Fire Cave looks much different from the other caves. It has two floors. Fire Chickens are present on the first floor while Fire Boars are present on the second floor. There is also a chest containing Fire Tusks, Diamonds, and a Fire Gem on the second floor. | Starting Island, in stone part, random place. |
| Yeti Cave | The Yeti Cave contains four respawning Yetis and also several plants which drop Ice Berries. There are 2 Chests containing Enchanted Shield in one, and Ice Arrow*3 in another. | Starting Island, in stone part, random place. |
| Halloween Cave | The Halloween Cave contains a Fire Boar which does not respawn, and, if searched, unlocks Pumpkin seeds. There is also a floating ghost which cannot be interacted with, and some Jack'o'lanterns. | Starting Island |
| Gold Golem Cave | The Gold Golem Cave changes every time it is entered, and thus is an endless source of Coal, Iron, Quartz, Gold and Diamonds. There is also a chest containing Titanium x2 at the bottom left or right corner. The cave also contains numerous Gold Golems which drop Gold. | Starting Island, in stone part, random place. |
| Wyrm Den | Contains the Wyrm Queen boss and 2 chests containing 1 spirit gem each, along with several pre-spawned Wyrms and all the Wyrms that the Wyrm Queen spawns. (See Wyrm Queen in bosses) | magic island, near the east sea, dig down and you will see it. |
| Ice Cave | Contains 2 accessible Yetis and 2 Yetis at the top of the cave, an Unknown Enemy that drops 1 Ice Heart and 3 Chests on 3 different rooms. The first chest contains 10 Ice Arrows, the second chest contains 1 Ice Sword and the third chest contains 1 Ice Shield. The background there is ice and snow. The ice background only lets you go in a straight line, making the cave hard to go through. The pillar for Ice Shield can also be found where the chest containing Ice Shield is found. | On the floating island in the magic island while wearing spirit goggles |
| Minotaur Maze | It changes every time you enter it. It is a maze made of the purple blocks, some of which shoot fireballs. Contains the minotaurs. The exit is randomized as well, and leads to the Minotaur Island. | On Sunset Haven near the firestone layer. |
| Wyrm Maze | A maze which has some chests that contain Spirit Gems, Blueprints, and which has shortcuts to many places. | On the top left corner of the Wyrm Den, after killing the boss |
| Water Cave | A cave containing water, which is connected to the ocean west of Sunset Haven. The Sub Pen is built here, after completion of the quest Water Cave. | Top left portion of the desert on Sunset Haven. |
| Fire Ant Cave | Newgrounds only. Has fire ants inside, which, when captured with a net, will turn into the antpanion familiar | Starting island |
| Colony Ship Hold | Has Titanium chests, Titanium, and Mecha-Scorpions | Sunset Haven, near Mirrow's lab |
| Colony Ship Logs | Has Diode Wolves on first level, Gunners on the second, and Ship's logs and a caged diode wolf on the third | Colony ship, directly under Mirrow's lab |