Story Bosses
- Mist Dragon
- General, Soldiers x3
- Octomammoth
- Antlion
- Mom Bomb
- Scarmiglione, Milon x4
- Scarmiglione Zombie
- Dark Knight
- Guardx2
- Yang
- Baigan
- Cagnazzo
- Dark Elf
- Sandy, Cindy, Mindy
- Barbariccia
- Calcax3, Brinax3 or Calcabrina
- Golbez
- Dr. Lugae, Barnabas or Barnabas-Z
- Lugaborg
- King Eblan, Queen Eblan
- Rubicante
- Demon Wall
- Scarmiglione Zombie, Cagnazzo, Barbariccia or Rubicante
- Attack Node, CPU, Defense Node
- Zeromus
Optional Bosses
- Asura
- Leviathan
- Odin
- Bahamut
- White Dragon
- Dark Bahamut
- Lunasaur
- Plague
- Ogopogo
- Thumbingway
- Storm Dragon (GBA Only)
- Gigas Worm (GBA Only)
- Master Flan, Black Flan x2, White Mousse x2 (GBA Only)
- T-Rex (GBA Only)
- Death Mech (GBA Only)
- Geryon (DS Only)
- Proto Babil (DS Only)
Lunar Ruins (GBA Only)
- Soldier Monkx8
- Lunar Titan
- Lunar Shiva
- Shiva
- Ifrit
- Titan
- Ramuh
- Lunar Dragon
- Lunar Odin
- Lunar Asura
- Lunar Ifrit
- Lunar Bahamut
- Lunar Ramuh
- Lunar Leviathan
- Bachioraidos
- Zeromus EG
