The Glowing Mushroom Cave (光っキノコ洞窟, Hikakkinoko Dōkutsu) is a large underground cavern located in the Land of Rainfall. The cavern possess a unique ecological system consisting of mainly bioluminescent flora and fauna. Prior to being discovered, no human had ever set foot into the cave system. During the Second Shinobi World War, the genin members of Team Cho Li took shelter here after being caught behind enemy lines and being separated from their sensei. Despite being a cave system, it holds a complex ecosystem with many different species of animals, plants and fungi.
- The Bright Moss () is a bioluminescent moss that grows on the ceiling of the cave system, acting as a light source.
- The Blue Glowing Mushroom () is a medicinal fungus that can be ground up and made into a paste that helps to numb pain. Can also be eaten but has been noted to taste terrible and is not very nutritious. By grinding it up and mixing it with the blood of a White Eel, an antidote to Blind Salamander poison can be created.
- The Red Glowing Mushroom (), unlike its blue counterpart, is poisonous and cannot be used for medicine or be eaten. If eaten it causes nausea and vomiting.
- The Blind Salamander () as its name implies, is a species of salamander that lacks eyes that is about 30 cm long. Its skin is highly poisonous and cannot be eaten as Kotarō found out.
- Bone Fish () are small, pale-white colored fish with red eyes and are about 3 cm long. There were noted by Takeo to be too small to eat.
- The White Eel () is a species of eel that lives in the vast lake near the Mushroom Grotto. At about 60 cm, it is the largest animal in the cave system. It is also the capable of eating the Blind Salamander, allowing its blood (when mixed with the Blue Glowing Mushroom) to act as an antidote to the salamander's poison.
- The Mushroom Grotto ()