These bosses are listed in the order that you should come across them in the game.

• Light World
  • Hyrule Castle
    • Ball and Chain Trooper
  • Eastern Palace
    • Armos Knights
  • Desert Palace
    • Lanmolas
  • Mountain Tower
    • Moldorm
  • Hyrule Castle Tower
    • Agahnim
• Dark World
  • Dark Palace
    • Helmasaur King
  • Watergate Dungeon
    • Arrghus
  • Skull Palace
    • Mothula
  • Gargoyle's Domain
    • Blind the Thief
  • Ice Island
    • Kholdstare
  • Misery Maze
    • Vitreous
  • Turtle Rock
    • Trinexx
  • Ganon's Tower
    • Agahnim
  • Pyramid of Power
    • Ganon