Twin-Goryas - Root Dungeon Mini Boss
Strategy: Use your sword. Spin attacks help.
Aquamentus - Root Dungeon Boss
Strategy: Avoid his fireballs, and keep your distance when he is flying. To defeat Aquamentus, strike him in the head just after he lands near the doorway on the right side of the room.
Facade - Snake Remains Mini Boss
Strategy: Drop bombs between Facade's eyes. It should take four direct hits to defeat him.
Dodongo - Snake Remains Boss
Strategy: Drop a bomb just in front of Dodongo so that he swallows it. If you do it right, he will be stunned for a few seconds. Pick him up while he is stunned using the Power Bracelet and toss him onto the spikes in the middle of the room.
Squiddies - Poison Fang Grotto Mini Boss
Strategy: To defeat the squids, pick them up from the small pools of water using your Power Bracelet and toss them away from the water, then slash them with your sword. After repeating this a few times with each squid, they will be defeated.
Mothula - Poison Fang Grotto Boss
Strategy: Dodge Mothula's attacks, and when he slows down in the middle of the room, slash him with your sword repeatedly.
Agahnim - Dragon Dance Dungeon Mini Boss
Strategy: Just like in Link to the Past, Agahnim has two clones of himself to assist him, which cannot be damaged. To pick out the true Agahnim, look for the wizard who casts a shadow. To defeat them, make sure both torches are lit at all times, and strike the true Agahnim with your sword.
Ghoma - Dragon Dance Dungeon Boss
Strategy: To defeat Ghoma, first concentrate on his huge claw. Keep your distance, and slash at the claw with your sword when it is safe to do so. Do not allow him to pick you up with the claw, as you will take quite a bit of damage if that happens. After you destroy the claw, equip your slingshot and shoot seeds at Ghoma's eye when it is open.
Syger - Unicorn Cave Mini Boss
Strategy: To defeat Syber, avoid him when he turns into a spiked ball, and when he emerges as a tiger, strike him on the tip of his tail with your sword.
Digdogger - Unicorn Cave Boss
Strategy: Use the Magnetic Gloves to pull the giant spiked ball into the Digdogger. After he has taken enough damage, Digdogger will split into several smaller creatures, which can be defeated with either the sword, or more attacks with the spiked ball.
Vire - Ancient Ruins Mini Boss
Strategy: To defeat Vire, first avoid the blue beams he shoots at you, then hit him with a spin attack. After he has taken enough damage, Vire will split into two smaller creatures. Again, defeat them with your sword.
Manhandla - Ancient Ruins Boss
Strategy: Manhandla can be defeated with the Boomerang. Start out by hitting the mouth-like flowers with the Boomerang. After a few hits, each flower will disappear, and Manhandla will start to move a little faster. After the last flower has been destroyed, strike the stem rapidly with the Boomerang, and when the core is revealed, slash it with your sword to finish off the boss.
Two Poes - Adventurer's Tomb Mini Boss
Strategy: The most important thing to remember when facing the two Poes is to keep the torches lit at all times. If they all are extinguished, you will be warped back to the beginning of the dungeon. The Poes themselves are not very difficult at all, as they can be defeated with a simple sword attack.
Gleeok - Adventurer's Tomb Boss
Strategy: To defeat Gleeok, use Roc's Cape to avoid the fireballs he shoots at you from time to time and strike his heads with your sword when you have a chance. After the heads have been destroyed, Gleeok will begin to jump around the room. Use Roc's Cape to jump just before he lands to avoid being stunned for a few seconds. Attack Gleeok with your sword just after he hits the ground.
Frypolar - Underworld Dungeon Mini Boss
Strategy: When Frypolar is in his fire state, use your Slingshot to shoot him with a Mystery Seed. This will change Frypolar to his icy state. Shoot him with an Ember Seed when he is still cold. After repeating this process for a while, Frypolar will be defeated.
Medusa Head - Underworld Dungeon
Strategy: Avoid the attacks of Medusa Head and attack with the sword when you have a chance. It shoots beams across the entire room, so you will want to equip Roc's Cape in order to avoid them.
Onox - Tower of Darkness Boss
Strategy: Use Roc's Cape to jump over Onox's attacks, and then attack him with a spin attack. After he takes enough damage, he will summon Din, still surrounded by the giant crystal, to be a shield for him. Use the Rod of Seasons to knock the crystal away and continue to attack Onox with spin attacks. After he takes enough damage, he will disappear. If you have the L2 Heart Ring equipped, you can walk around the room in circles for a little while to restore your health completely. When you are ready to face Onox's final form, approach the crystal, and the floor will crumble, causing you to fall into another chamber.
Onox's Final Form - Tower of Darkness Boss
Strategy: Onox's final form is the most difficult boss in the game. To finish him off, you will need to use Roc's Cape to jump on one of his hands when he swipes at you. Ride his hands and jump towards his head, then slash at the crystal on his forehead. If you can, try to jump to the other hand because it will save you a lot of time, trouble and health because you can immediately jump back and attack Onox again. The best advice is to keep moving, as you will avoid more of his attacks that way, and if you have the L2 Heart Ring equipped, moving around helps you restore your life. When Onox attacks by swiping across the entire screen with one of his claws, quickly move to the other side of the screen, using a Pegasus Seed if necessary. After enough hits to the crystal on his forehead, Onox will be defeated.