The Legend of Zelda Phantom Hourglass Walkthrough part 19

Boss: Cyclok, Stirrer of Winds.

To beat this boss, throw bombs into the cyclone, when Cyclok's shadow moves over it. When he falls down, hit him with your sword. You can also throw bombs into the cyclones that are summoned by Cyclok.
Cyclok may also drop to the surface and charge at you (which he didn't do in the video). When he does that, you can't throw bombs at him, so dodge this attack.