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The Wind Fish is the creator and deity of Koholint Island in Link's Awakening. He is a multi-colored whale with large angel-like wings. Throughout most of the game, he resides within his Egg atop Mt. Tamaranch that can only be awakened by playing the Ballad of the Wind Fish on the Eight Instruments of the Sirens.
Ocarina of Time
Great Deku Tree
The Great Deku Tree is the guardian deity of the Kokiri in Ocarina of Time. He is the keeper of the Kokiri's Emerald. He appears to possess much knowledge as he tells Link about the Golden Goddesses and Ganondorf. His power pales in comparison to Ganondorf's. However, Ganondorf had the ability to defeat him with a curse. The Deku Tree is reborn as the Deku Tree Sprout and keeps all of the Great Deku Tree's knowledge. Therefore, the Deku Tree is semi-immortal.
The Fierce Deity is the ultimate form Link takes in Majora's Mask. Link can only do this if he obtains all the masks available in the game. Due to his brief appearance, much is unknown about the Fierce Deity. It is likely he is related to the moon, as he has a crescent moon emblazoned on his tunic.
The Giant Turtle that transports Link to the Great Bay Temple in Majora's Mask appears to be a deity of some sort as he knows of what is going on in the ocean, and knows of Link's name and quest before he tells him. After Link frees the third Giant, the Turtle remarks that he must return to his slumber once more.
The Wind Waker
Hylia is the deity worshipped by the people of Skyloft. She later abandoned her divinity and was reincarnated as a mortal.