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By the order in which you fight them:
The Legend of Zelda- Aquamentus
- Dodongo
- Manhandla
- Gleeok
- Digdogger
- Gohma
- Gannon
- Horsehead
- Helmethead
- Rebonack
- Carock
- Gooma
- Barba
- Thunderbird
- Dark Link
- Armos Knights
- Lanmolas
- Moldorm
- Agahnim
- Helmasaur King
- Arrghus
- Mothula
- Blind
- Kholdstare
- Vitreous
- Trinexx
- Ganon
- Dark Links (GBA only)
- Moldorm
- Genie
- Slime Eyes
- Angler Fish
- Slime Eel
- Façade
- Evil Eagle
- Hot Head
- Nightmare
- Giant Hardhat Beetle (DX only)
- Queen Gohma
- King Dodongo
- Barinade
- Phantom Ganon
- Volvagia
- Morpha
- Bongo Bongo
- Twinrova
- Ganondorf
- Ganon
- Odolwa
- Goht
- Gyorg
- Twinmold
- Majora
- Majora's Mask
- Majora's Incarnation
- Majora's Wrath
- Pumpkin Head
- Head Thwomp
- Shadow Hag
- Eyesoar
- Smog
- Octogon
- Plasmarine
- Ramrock
- Veran
- Twinrova (secret boss)
- Ganon (secret boss)
- Aquamentus
- Dodongo
- Mothula
- Gohma
- Digdogger
- Manhandla
- Gleeok
- Medusa Head
- General Onox
- Dark Dragon
- Twinrova (secret boss)
- Ganon (secret boss)
- Deguchitato
- Derazoru
- Gouen
- Vaati
- Gohma
- Kalle Demos
- Gohdan
- Helmaroc King
- Jalhalla
- Molgera
- Puppet Ganon
- Ganondorf
- Phantom Ganon
- Stone Arrghus
- Helmaroc King
- Jalhalla
- Dodongo
- Dagtail
- Frostare
- Big Dodongo
- Vaati
- Ganon
- Big Green ChuChu
- Gleerok
- Mazaal
- Big Octorok
- Gyorg Pair
- Vaati
- Vaati Reborn
- Vaati Transfigured
- Vaati's Wrath
- Diababa
- Fyrus
- Morpheel
- Stallord
- Blizzeta
- Armogohma
- Argorok
- Zant
- Possessed Zelda
- Ganon
- Horseback Ganondorf
- Ganondorf
- Blaaz
- Cyclok
- Crayk
- Diabolical Cubus Sisters
- Dongorongo
- Gleeok
- Eox
- Bellum
- Ghost Ship
- Bellumbeck
- Stagnox
- Fraaz
- Phytops
- Cragma
- Byrne
- Skeldritch
- Demon Train
- Chancellor Cole
- Malladus
- Darknut
- Stallord
- Beetle Lord Death Bug
- Captain Stalfos
- Bana Bana
- Beetle King Death Bug
- Dora Dora
- Uncle Rupee
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