In Phantom Hourglass, Flying Fish are one of the easiest of all the water creatures to defeat. These Fish will just hover above the water before attempting to run into the SS Linebeck. A single shot from the ship's Cannon will immediately defeat these creatures.
In the Phantom Hourglass manga by Akira Himekawa, a Flying Fish leaps out of the water to attack the SS Linebeck. Unlike in the game, the Flying Fish spits a rock at the ship, almost capsizing it. Link questions Linebeck if the ship has any kind of weaponry to fight it. As the Fish continues attacking the vessel, Linebeck replies that the ship does not. Link asks the captain how they are going to cross the ocean with Fish like these. Linebeck says by running for his life, speeding the SS Linebeck forward and leaving the Flying Fish behind.
After getting a Cannon from Eddo, the Flying Fish reappears. Link fires the Cannon and causes the Fish is explode.
Names in Other Regions
パタフライ (Pata Furai)
Combination of パタパタ (patapata), Japanese onomatopoeia for "flap flap" or "flutter" and フライ (furai) meaning the English word "fly" or "fry".