There are different Pokémon Languages seen in Pokémon Mystery Dungeon media, mostly in various written forms. This page covers all known forms of communication in Pokémon Mystery Dungeon. From footprint-shaped writing to its ancient counterparts and even long-forgotten texts written in Unown characters.
Ancient Footprint Runes
Ancient foot-shaped writing has been left by Pokémon of the past in the Voidlands and around the Pokémon world. Unlike most other Pokémon, the partner character in Super Mystery Dungeon is able to fluently read them. Mawile studies this form of writing.
"Should you hope to overcome this crisis, summon a person. A person will have the power to break the barrier over the spring. You must summon a person from the world of humans."
Cave of the Deep entrance
"These are the Voidlands. The spirits of Pokémon that have been turned to stone are locked away here."
"Enemy Pokémon in the Voidlands are not real Pokémon. They are all apparitions made up of hate and given physical form. We must continue onward to defeat them."
Cave of the Deep exit
"Why do Pokémon become stone? Dark Matter is the source of all woe. Dark Matter absorbs the energy of Pokémon as it turns them to stone. With that energy, it grows stronger. Dark Matter will continue to turn Pokémon to stone to enlarge itself."
"Look out for Void Shadows! Void Shadows will make Pok-"
Calm Craggy Area exit
"Somewhere in this world, there exists a Tree of Life. That Tree of Life has become possessed by Dark Matter. As it grows, Dark Matter snatches away the vitality of the Tree of Life. If this continues, the Tree of Life will wither and die. We must do something..."
"At last you've made it here. Just beyond here, at the top of Reverse Mountain, is the door to hope. A path of light that connects to the world you once knew. It is an exit from these Voidlands. However, there is a problem. A countless number of Void Shadows are blocking the light from above the ground. The power to defeat these Void Shadows...is unfortunately not something I posses. And so I will wait here. Judging by the position of the stars, Dark Matter should stop momentarily... Dark Matter is related to the movements of the astronomical bodies. If everyone fighting back against Dark Matter in the world...can somehow protect the Tree of Life...Dark Matter will cease, and the end of the world will be averted. And I will be able to leave this place... In other words, I'll be able to return from being stone. However, even if I were to get out of here, the fight would not end there. I must prepare. For the distant future..."
The text in this area isn't directly read by the characters.
Ancient Unown language
An ancient Unown language is seen in the Hidden Land in the Explorers titles and Pokémon Mystery Dungeon: Explorers of Sky - Beyond Time and Darkness. Grovyle and his his human partner have studied this language together in the past.
"KASUG AP EI
For the anime episodes OLM took the same approach they've been using for the main series Pokémon anime. In Pokémon Mystery Dungeon: Explorers of Time and Darkness (Anime) various unidentified characters are used. In Pokémon Mystery Dungeon: Gates to Infinity (Anime) they instead used the more standardized characters that they've been using since 2010. This latter form of writing is a substitution cipher for the Latin alphabet.
Request Board in Pokémon Paradise
Pokémon seem to mostly write in footprint runes (Japanese: あしがたもじ) (referred to as foot-shaped writing in Pokémon Super Mystery Dungeon in English), which is a writing script-based on various Pokémon footprints, apparently arranged in different directions. Footprint runes are first mentioned by the partner in the Explorers titles when the Groudon statue in Foggy Forest is found. Footprint runes can also be seen on Grovyle's outlaw notice.
Groudon statue in Foggy Forest
"Reignite the life that burned within Groudon... Then the sky shall blaze with the sun's heat... The path to treasure shall be revealed."
Old Ruins Murals
Footprint runes can be seen on the Old Ruins murals leading to the Rainbow Stoneship. The runes themselves are not commented on, and it's not known if they match their current counterparts. The Rainbow Stoneship just outside the ruins uses Unown characters instead of footprint runes.
Jynx can speak their own language that other Pokémon can't understand, as seen when talking to Jynx inside a dungeon in / Pokémon Mystery Dungeon: Red and Blue Rescue Team, where it is represented with various characters. Unfortunately, when speaking to Jynx as another Jynx, the text remains the same. It should be noted that a few Pokédex entries in the main series state that Jynx speak in a language similar to humans'; thus, the implication is that the Pokémon in this game can't understand human languages or those similar to humans', like Jynx's.
Beldum can communicate with others using magnetism. This is represented in Red and Blue Rescue Team with plus and minus symbols.
Squiggly characters can be seen on the Rescue Team artwork for Pokémon News, Pelipper's notice in Gates to Infinity, and the Pokémon News model in Rescue Team DX. This writing seems to be associated with Pelipper.
In Other Languages
-  Anime Language on pocketmonsters.net