Like every other Pokémon game, Pokemon Mystery Dungeon: Gates to Infinity comes with a myriad of different Pokémon. While not every Pokémon seems to be available, multiple different species are still available. They are as follows
Boss Pokémon
The following Pokémon aren't recruitable, but are battleable through various special missions in Companion Mode and Local Play or within the storyline.| No. | Pic | Name | Type |
| #249 |
|
Lugia ルギア |
  |
| #250 |
|
Ho-Oh ホウオウ |
 |
| #643 |
|
Reshiram レシラム |
 |
| #644 |
|
Zekrom ゼクロム |
 |
| #646 |
|
Kyurem キュレム |
 |
| #646 |
|
Kyurem キュレム |
|
| #646 |
|
Kyurem キュレム |
|