Parasite Queen
The first boss in Metroid Prime, the Parasite Queen is located on the Space Pirate Frigate in the main reactor. It is surrounded by rotating shields and fires acid from its mouth. Plug missiles and beam shots into its mouth to defeat it.
Flaahgra
Flaahgra is a large mutated plant that is the source of the poisonous waters in the Chozo Ruins. It is surrounded by four dishes that reflect sunlight and needs constant solar energy. Its roots are its weak spot. Flaahgra gives up the Varia Suit when it's defeated, which protects Samus from super-heated areas in Magmoor Caverns.
Thardus
Thardus is an experiment created by the Space Pirates who used Phazon on a group of rocks, but the Pirates gave up trying to pacify it since it became too dangerous. Thardus has the ability to control the weather, roll into a ball, hurl large rocks, and encase enemies in ice. It resides in a Quarantine Cave in the Phendrana Drifts. Defeating Thardus gives you the Spider Ball.
Omega Pirate
The Omega Pirate resides in the Phazon Mines. It is an extremely large Elite Pirate which is able to become invisible and regenerate health. It is considered by many fans to be one of the game's toughest bosses. It attacks with its powerful hands, a Wave Quake Generator, and a Missile Launcher. Defeating the Omega Pirate gives Samus the Phazon Suit, which protects her from blue Phazon damage.
Meta Ridley
The fight with Meta-Ridley occurs above the crater in the Tallon Overworld. Meta-Ridley has two forms: a flying form and ground form, who uses a number of weapons and melee attacks. His weak spot is the gem on his chest.
Metroid Prime
The final boss of the game. It exists in two forms: the first being a spider-like creature with mainly projectile attacks. This form is weak against Power Beam if yellow, Wave Beam if blue/purple, Ice Beam if white, and Plasma Beam if red. The second form being a hovering, ethereal tentacled entity, sort of like a clear blue squid with bright menacing yellow eyes. Stand in the pools of Phazon it creates and blast it with your new Phazon Beam.