| Pokemon Name | Pokemon Level | Location |
| Espeon | Level 25 | Starter |
| Umbreon | Level 26 | Starter |
| Makuhita | Level 30 | Minor B Peon Trudly |
| Bayleef | Level 30 | Mystery Troop Verde (Phenac City) |
| Quilava | Level 30 | Mystery Troop Rosso (Phenac City) |
| Croconaw | Level 30 | Mystery Troop Bluno (Phenac City) |
| Furret | Level 33 | Rogue Cal (Pyrite Town) |
| Misdreavus | Level 30 | Rider Vant (Pyrite Town) |
| Noctowl | Level 30 | Rider Nover (Pyrite Town) |
| Flaafy | Level 30 | Street Performer Diogo (Pyrite Town) |
| Skiploom | Level 30 | Rider Leba (Pyrite Town) |
| Quagsire | Level 30 | Bandana Guy Divel (Pyrite Town) |
| Slugma | Level 30 | Rollerboy Lon (Pyrite Town) |
| Yanma | Level 33 | Cipher Peon Nore |
| Remoraid | Level 20 | Minor B Peon Reath |
| Mantine | Level 33 | Minor B Peon Ferma |
| Quilfish | Level 33 | Hunter Doken |
| Medidite | Level 33 | Rider Twan |
| Dunsparce | Level 33 | Rider Sosh |
| Swablu | Level 33 | Hunter Zato |
| Sudowoodo | Level 35 | Cypher Admin Minor B |
| Plusle | Level 13 | Receive from Duking |
| Hitmontop | Level 38 | Cipher Peon Cowap |
| Entei | Level 40 | Cipher Admin Dakim |
| Ledian | Level 40 | Cipher Peon Kloak |
| Suicune | Level 40 | Cipher Admin Venus |
| Gligar | Level 43 | Hunter Frena |
| Stantler | Level 43 | Chaser Liaks |
| Piloswine | Level 43 | Bodybuilder Lonia |
| Sneasel | Level 43 | Rider Nelis |
| Aipom | Level 43 | Cipher Peon Cole |
| Murkrow | Level 43 | Cipher Peon Lare |
| Forretress | Level 43 | Cipher Peon Vana |
| Ariados | Level 43 | Cipher Peon Lesar |
| Granbull | Level 43 | Cipher Peon Tanie |
| Vibrava | Level 43 | Cipher Peon Remil |
| Raikou | Level 40 | Cipher Admin Ein |
| Delibird | Level 45 | Cipher Peon Arton |
| Sunflora | Level 45 | Cipher Peon Baila |
| Heracross | Level 45 | Cipher Peon Dioge |
| Skarmory | Level 47 | Snagem Head Gonzap (Realgem Tower) |
| Miltank | Level 48 | Bodybuilder Jomas (Tower Colosseum) |
| Absol | Level 48 | Rider Delan (Tower Colosseum) |
| Houndoom | Level 48 | Cipher Peon Nella (Tower Colosseum) |
| Tropius | Level 49 | Cipher Peon Ston (Tower Colosseum) |
| Metagross | Level 50 | Cipher Nascour (Tower Colosseum) |
| Tyranitar | Level 55 | Cipher Head Evice (Tower Colosseum) |
| Smeargle | Level 45 | Team Snagem Biden |
| Ursaring | Level 45 | Team Snagem Agrev |
| Shuckle | Level 45 | Deep King Agnol |
| Togetic | Level 20 | Shady Guy (Outskirt Stand) |
| Pikachu | Level 10 | Silver Poke Coupon Card (Gift Pokemon) |
| Ho-oh | Level 70 | Catch all Shadow Pokemon and purify them. Use Pokemon from Story Mode to beat Mt. Battle in Colosseum Mode. |
| Jirachi | Level 5 | From Bonus Disc |
