Angel Island Zone features two boss encounters: a mini-boss in Act 1 and Dr. Robotnik's main boss in Act 2. Both are relatively straightforward but serve as an introduction to the game's boss mechanics.

Mini-Boss: Flame Mobile
- Location: Angel Island Zone Act 1
- Description: A small, wheeled robot with a flamethrower.
- Attack Pattern: Moves back and forth across the screen. Periodically stops and fires a stream of fire horizontally.
- Strategy: Wait for the Flame Mobile to stop firing. As soon as its flame attack ends, jump and hit its cockpit. It will then retreat and repeat its pattern. Three hits are sufficient to destroy it. Be careful not to get caught in its flame, as it can push you back and cause damage.
- Weakness: Cockpit when not firing.
- Reward: Clear path to the next section.
Boss: Egg Mobile (Flamethrower)
- Location: Angel Island Zone Act 2
- Description: Dr. Robotnik in his Egg Mobile, equipped with a large flamethrower.
- Attack Pattern: Flies across the top of the screen, then drops down to unleash a long burst of fire. He will often try to position himself directly above you before firing.
- Strategy: The key is to attack Robotnik when he is rising after his flame attack or when he is moving across the top of the screen. Avoid his flame by moving quickly to the side. Use a Spin Dash to build speed for a higher jump if needed. Seven to eight hits will defeat him.
- Weakness: Robotnik's cockpit.
- Reward: Progress to Hydrocity Zone.