Empress Bulblax
You first encounter Empress Bulblax in the Hole of Beasts. She resembles a rotund worm. To defeat her, throw Pikmin at her head until she faces front. Call the Pikmin back, wait for Empress Bublax to finish rolling and repeat this attack until you defeat her.
Burrowing Snagret and Pileated Snagret
The Burrowing Snagret is a bird's head that pops up from the ground. The Pileated Snagret comes all the way out of the ground. Defeat both by throwing Pikmin at the Snagret's head when it comes up slowly. When the Snagret pops up quickly, call the Pikmin away to keep them safe and wait for another chance to attack.
Beady Longlegs, Man-At-Legs, and Raging Longlegs
The Beady Longlegs, Man-At-Legs, and Raging Longlegs are large, spiderlike creatures. Throw Pikmin at the center of the body of the spider when it hovers near the ground. Call the Pikmin away when the spider again rises and repeat the attack until you defeat these bosses. Watch out for the stomping feet of the Beady Longlegs and Raging Longlegs and lasers of the Man-At-Legs.
Giant Breadbug
The Giant Breadbug is, as its name implies, a walking loaf of bread. It first appears in the Gluttons Kitchen. Wait for the bug to grab an item and start pulling it away. Direct your Pikmin to hold onto the item. Make as many Pikmin as possible hold on to the item. They will drag the bug to the space ship, killing it.
Emperor Bulblax
Emperor Bulblax resembles a bloated ladybug. You first encounter him in the Bulblax Kingdom. Throw as many Pikmin as possible as quickly as possible into the space between his eyes to defeat him.
Waterwraith
You first encounter the Waterwraith in the Submerged Castle. This boss resembles a frog that's pushing a cylindrical piece of stone. You can injure this boss only on Level 5 of the Submerged Castle. Throw the purple Pikmin at the Waterwraith, which will freeze if the purple Pikmin touches it. Defeat the boss by continuing to throw the purple Pikmin at the Waterwraith.
Raging Bloyster
The Raging Bloyster, found in the shower Room, resembles a slug. Continually switch between Captains Olimar and Louie to confuse it while you throw Pikmin at its tail to defeat it.
Segmented Crawbster
This boss looks something like a crab. You first encounter it in the Cavern of Chaos. Lure the Crawbster to a wall. It will hit the wall and flip over, giving you the opportunity to throw Pikmin at its vulnerable underside.
Titan Dweevil
The Titan Dweevil is the last boss, found in the Dream Den. It has four weapons. Use certain Pikmin to defeat certain weapons, eventually defeating the entire boss. For example, use the red Pikmin to defeat the Flare Cannon, the white Pikmin to defeat the Chemical Weapon and the blue Pikmin to defeat the Monster Pump.