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I compiled the list of all the monsters in the Zelda series and also every boss. Also, the parenthesis indicate different versions of the monster.

The Legend of Zelda Complete Monster and Bosses List
Monsters
A
Ache, Acheman, Acro-Bandits, Aeralfos, Anti-Faeries, Anti-Kirby, Anubis, Arm Mimics, Armos (Death, Statues)

B
Baba Serpent, Babusu, Baby Gohma, Bago Bago, Ball and Chain Soldier, Bari, Basilisk, Bat (Evil, Bad, Battle), Bazu, Beamos (White), Bee, Beetle (Spiny, Spiked, Scissors, Hardhat), Big Baba, Big Bot (King), Big Skull, Biri, Bit, Blaino, Bloober, Bob-Omb, Boe (White, Black), Boko Baba, Bokoblin, Bomb Eater, Bombarossa, Bombite, Bombfish, Bombling, Bomskit, Boo Buddies, Boon, Bot, Boulder, Bubble (Red, White, Blue, Green, Fire, Ice), Bug, Bulblin Infantry, Bulblin Riders, Bulblin Warrior, Buzzblob (Giant) *Bloat*

C
Cactus, Candles, Cannon Boat, Captain Keeta, Chain Chomp, Chaser, Cheep Cheeps, Cheep Sheep, Chilfos, Chu Chu (Chu, Chu Worm, Blue, Red, Green, Yellow, Dark, Rock, Spiny, Big Green, Big Blue), Cloud Piranha, Clutch, Crab, Crow, Cue Ball, Cukeman

D
Daira (Red), Dangoro, Dark Hammer, Dark Link, Dark Nut (Mighty, Royal, Red, Black Knight), Dead Rock, Dealer (Blue), Death Sword, Decid Hand, Deep Python, Deku Baba (Bio, Mini), Deku Scrub (Business, Mad Scrub), Deku Toad, Desbreeko, Desert Specter, Dinofos, Dixiehands, Dodongo (Baby, Big), Dodongo Larvae, Dodongo Snakes, Doomknocker, Door Mimic, Dragonfly

E
Eagle Knight (Blue), Eeno, Eye, Eye Brute, Eye Plant, Eye Slug, Eyeball Monster, Eyegore (Statues)

F
Fake Doors, Fire Cephalopod, Fire Toadpoli, Floormaster, Flower, Flying Fish, Flying Unicorn, Flying Pots, Freezar, Freezard (Mini) Frypola

G
Garo (Master), Gekko, Gel (Giant), Geldarm, Geldmen, Gerudo, Ghini (Giant), Ghost, Ghoul Rat, Giant Bee, Gibdo, Gohma Larvae, Gomess, Goomba, Goriya, Grim Creeper, Guay, Gyorg

H
Hammer Thrower, Head, Helmarok, Helmasaur, Helmasaurus, Hinox, Hiploops, Hoader, Hokkubokku, Hue, Hylian Hornet, Hyrulean Soldiers

I
Igos Du Ikana, Iron Knuckle (Red, Blue), Iron Masks

J
Jellyfish, Jolene, Jolene’s Ship

K
Kanalet Soldiers, Kargorok, Keaton, Keese (Fire, Ice), King Bulblin, Kodondo, Kotake, Koume, Ku, Kurubo

L
Lakitu, Lanmola, Leever, Like Like (Rupee Like, Deku Like), Lizafos (Skull-Face, Axe-Tail), Lizard, Lizardmen, Loach, Lowder, Lynel

M
Madderpillar, Mad Bomber, Magician, Mago, Magtail, Mangned, Mask-Mimics, Megmet, Mimic, Mini Cyclone, Mini-Moldorm, Miniblin, Moa, Moblin (Bow, Spear, King, Club), Moby, Moldorm, Moldworm, Mole, Monkey, Monster, Morth, Mothula, Mulldozer, Mutt, Myu

N
Nejiron, Nuranuru

O
Octorok (Big Octo, Golden, Flying, Ocean, Octoballoon), On/Off, Ook, Oopoonga, Orange Skull Head

P
Patra, Pariodd, Peahat, Peahat Larvae, Pengator, Pesto, Phantom, Phantom Eye, Phantom Riders, Phantom Zant, Pickitt, Pig Warriors, Pincers, Pirates, Pirate’s Ship, Poe (Sisters (Amy, Beth, Joelle, Meg) Big, Imp), Pokeys, Poison Mite, Pols Voice, Popo, Puffstool, Puppet

R
Rat, Rat Head, Raven, Real Bombchu, Reapling, ReDead, River Devil, Rock, Rolling Bones, Rollobite, Ropa, Rope (Golden), Royal Guard

S
Sandworm, Scorpion, Sea Trap, Sea Urchin, Seahat, Shabom, Shadow Bot, Shell Beast, Shell Blade, Shell Spinner, Shy Guy, Skeleton, Skull Rope, Skullball, Skullfish, Skullkid, Skulltula (Big, Golden, Pygmy), Skullwalltula, Slarok, Slime (Green) Sluggula, Smasher, Snake (Rope), Snap Dragon, Snapper, Soldiers, Soprano, Spark, Spider, Spike, Spikeball, Stag Beetle, Stal, Stalchild, Stalfos (Shrouded, Knights), Stalhound, Stalkin, Staltroop, Star, Statues, Stinger, Stone Hinox, Subterror, Swamola, Swoop

T
Tailparasaran, Takkuri, Tektike (Red, Golden), Tektile, Tentacle, Three of a Kind, Tile, Tile Worm, Toado, Toppo, Torch Slug, Trap, Trooper, Turtle, Turtle Rock, Twilit Baba, Twilit Bloat, Twilit Bulblin, Twilit Bulblin Archer, Twilit Carrier Kargarok, Twilit Kargarok, Twilit Keese, Twilit Messenger, Twilit Parastie, Twilit Vermin

U
Urchin

V
Vire, Vulture

W
Wallmaster, Water Cephalopod, Water Toadpoli, Winder, Wisp, Wizzrobe (Fire, Ice), Wolf Head, Wolfos (White), Wort

Y
Yook, Young Gohma

Z
Zant Mask, Zant’s Hand, Zirro, Zol, Zola, Zombie, Zora (Warrior)


Bosses A
Agahnim, Agahnim’s Shadow, Angler Fish, Aquamentus, Argorok, Armagohma, Armos Knights, Arrghus (Stone)

B
Ball and Chain Soldiers, Barba, Barinade, Bellum, Big Dark Stalfos, Big Moldorm, Big Octorok, Blaaz, Blind the Thief, Blizzeta, Bongo Bongo

C
Carock, Chief Soldier, Crayk, Cubus Sisters, Cyclok

D
Dethl, Diababa, Digdogger, Dodongo (King), Dongorongo

E
Eox, Evil Eagle, Eyesoar

F
Facade, Frostare, Fyrus

G
Ganon, Ganon’s Shadow, Ganondorf, Genie, Gleeok, Gleerok, Gohdan, Gohma, Goht, Gooma, Gyorg, Gyorg Pair

H
Head Thwomp, Helmarok King, Helmasaur King, Helmethead, Horsehead, Hot Head

J
Jalhalla

K
Kalle Demos, Kholdstare

L
Lanmolas, Lanmola’s Shadow

M
Majora (Mask, Incarnation, Wrath), Manhandla, Mazaal, Medusa Head, Moldorm, Moldorm’s Shadow, Molgera, Morpha, Morpheel Mothula

O
Octogon, Odolwa, Onox

P
Phantom Ganon, Plasmarine, Possessed Nayru, Pumpkin Head, Puppet Ganon

R
Ramrock, Rebonack

S
Shadow Hag, Shadow Link, Slime Eel, Slime Eyes, Smog, Stallord

T
Thunderbird, Trinexx, Twinmold, Twinrova

V
Vaati, Veran, Vitreous, Volvagia

Z
Zant, Zelda