Edited 21-3-2015
Of Gods:
Lesser Gods (A List)
Not the creator gods, but these guys still have punch. Note that I am treating Majora's Mask deities as Hyrulian ones – billed as either from other worlds or a land far away. Many of these are part of my head-canon.
SHADOW AND LIGHT
Ceilear (Dawn, Dusk)
Ceilear [Gaelic 'dawn'] is the daughter of Ujaal, and the goddess of twilight: both Dawn and Dusk. She may be the primary god of the Twilit Realm.
LIFE AND DEATH
Preta
Preta is Hyrule's equivalent of the boatman or Saint Peter – she receives the souls of the departed and sends them to their appropriate destination, whether it be the afterlife, reincarnation, or destruction. It is unknown if she is an avatar of or the daughter of Farore, but there is a very strong association.
WATER GODS
The sons of Uruisg.
Jabu-Jabu
Lord Jabu is the protector deity of inland waterways – rivers, streams, rain, and headwaters. He is the patron of freshwater Zora, and takes the form of a large grey whale.
Jabun (Sea Spirit)
Jabun is the god of harbours, and protector of islands and coasts. He is the patron of the sea-dwelling Zora, and appears as a great blue whale.
Linn-Bruadar (Wind Fish, Dreamer on the Seas, Levias)
Linn-Bruadar takes the form for a great winged whale, a bringer of rain. He travels the world by both land and sea, and acts as a protector spirit for wayward travelers, sealing them in his dream worlds until the time comes to wake and be rescued.
Oshus (Ocean King)
Oshus, Uruisg's eldest, is the Ocean King, lord of all great seas. He is an unpredictable god, prone to acts of great cruelty in one breath, and great kindness in the next. He is worshiped by sailors and islanders, but patron to none.
Oshus, like Linn-Bruadar, occasionally dreams other worlds, but is a world dreamed by a god truly a dream?
Turtle (Lord of Calm Water)
The Turtle is the patron god of seafaring travellers, maintaining safe passage in even the stormiest seas.
FIRE
Fire Dancers
Spirits of fire, the Fire Dancers are omens (and occasional causes) of wild fires, war, and volcanic eruptions.
The Mountain Goddesses (Daughters of Din)
Every mountain has its spirit and character. The Mountain Goddesses are the strongest of these, hailing from volcanoes.
EARTH
Goddess of Sand
She is an unnamed goddess whose dominion is the desert. She is the matron goddess of the Gerudo along with Farore. She is highly protective of her charges and her secrets and may be the spirit of Pehtey.
TREES OF LIFE
The descendants of Dekan, the Deku, Maku and Bagu Trees carry the memories of all their ancestors. Once they are no longer saplings and until they grow too old they are capable of 'uprooting' themselves and travelling.
Bagu
Descendants of Dekan, the Bagu Trees are malevolent gods of the forest – those who jealously guard their woods and turn harsh and spiteful measures against interlopers. They maintain the Lost Woods and all such unwelcoming forests.
Deku
The Deku Trees, Dekan's most powerful descendants, are the Forest Guardians and the guardians of Dekan's peoples, the Kokiri and the Koroks* to whom the Great Deku serves a fatherly/grandfatherly role. The Dekus are peaceful.
*Yes, it's hinted they are the same, but it seems odd that the Kokiri would change that much. Maybe they didn't survive the flood, but the Koroks – being wood and better at hiding themselves (and thus never before seen) – could float and survived even if they didn't make it to the mountains. Or the Koroks could well be young Deku or Maku.
Maku
Many lands have at least one guardian Maku tree. The Maku trees serve as living memories to the lands they live in and protector spirits to those who dwell on those lands - they do not limit themselves to forests and most often root down in fields.
WIND SPIRITS
Cyclos
God of storm winds and younger brother of Zephos. He takes the form of a large red frog that travels in storm clouds.
Valoo (Sky Spirit)
A great dragon, Valoo is the guardian of the skies and of the Rito peoples, to whom he grants wings when they come of age.
Zephos
God of the four winds and elder brother of Cyclos. He takes the form of a large pale blue frog that travels on clouds.
PROTECTOR DEITIES
Castor
A spirit of the land, Castor protects the Castor wilds in the form of a beaver.
Eldin
A Great Spirit of the earth and guardian of the plains of Eldin, from which his name comes. Eldin favours those with knowledge, and takes the form of a great bird of prey when he appears.
Faron
A Great Spirit of the earth and guardian of the forests of Faron, Faron favours those with wit, and takes the form of a large common long-tailed monkey.
Firone, Warden of the Woods, the Water Dragon
The dragon deity appointed by Hylia to guard the Faron region in her absence. She is also the patron of the Parella. (Name is the Japanese transliteration as the other Faron came first.)
Four Giants (Mountain, Valley, Swamp, Ocean)
The guardian deities of the land of Termina, which is connected to Hyrule – although connected by gate to another realm or just a distant part of the same world is uncertain. The Four Giants each watch a corner of their country, and represent the four cardinal directions – North, East, South and West – which sometimes serve as their names. They were once very active, but now sleep much of the time. They will come if called in times of need.
Hylia (Her Grace)
The mortal goddess – Hylia is the embodiment of Hyrule, daughter of Din, Farore and Nayru. Early in Hyrule's history Hylia surrendered her immortality in order to make use of her mothers' relic, the Triforce. It is believed that she has been reincarnated several times through the ages, and like the Golden Three she has an affinity for time, and may be able to appoint Heroes. Hylia was once known for being cruel with the sweetest of smiles.
Lanayru
A Great Spirit of the earth and guardian of Lanayru Plains around Lake Hylia and the smaller lakes there, Lanayru favours bravery, tempered but caution. He takes the form of a sea serpent.
Ordona
A Great Spirit of the earth, and guardian of the Ordon Highlands, Ordona favours those who are kind and determined, and takes the form of an Ordon goat.
Orudin, the Fire Dragon
The dragon deity appointed by Hylia to guard the Eldin region. (Orudin is a transliteration of the Japanese name as an Eldin province protector named Eldin was already extant.)
The Owl
The Spirit of the Wind Fish, his avatar within the dream worlds.
The Thunder Dragon, Ranel
The dragon deity appointed by Hylia to guard the Lanayru region. He is also a god of innovation and invention. (Ranelle is the Italian name.)
CHAOS
Bellum
A sea demon in the form of a hideous squid, Bellum is the nemesis of the Ocean King Oshus. He hunts those the King favours and haunts the realms of Oshus' dreams.
Demise
A great god of terror and destruction, Demise is the nemesis of Her Grace. The Heroic Cycles may have originated with his curse, but may have also pre-existed.
Ganon
The Boar God of Chaos, Ganon is an avatar of Mawt who frequently breaks into the living realms, causing death and destruction. He often uses pawns to help him re-enter Hyrule.
Majora
A mad spirit of Spite born of another world, Majora craves bringing destruction to all he passes. He was sealed inside of a mask at some point in the past.
Nightmare
A malevolent spirit and brother of Bellum, Nightmare serves Mawt by plaguing the dreams of gods and mortals alike. He often plagues the dreams of Linn-Bruadar, being to the Wind Fish's dreams what Mawt is to the waking world.
Shadow of the Brightest Light (the Shadow)
A being, born of the Dark Mirror, that takes the shape of one of the strongest mortal or semi-mortal beings of light in the region. This has led to the legends of the Hero's Shadow, as the Heroes, Sages and Royals are usually the most powerful Light-dwellers.
Vaati
Formerly a Minish (Picori) Wind Sorcerer, Vaati was tempted by Ganon and became his foremost acolyte, and then his disciple. He later ascended as a wind demon. Now a god of sudden storms, he yearns to tear down the world with his howling winds.
FAIRIES
Butterfly (Spirit of Kindness)
A Virtue, she is known to confer blessings on those who show generosity
Dragonfly (Spirit of Wit)
A Virtue, she blesses those who show sharp wit or wisdom.
Great Fairies
Powerful fay beings with the power to confer healing, power, blessings and curses. Great Fairies often have aspects or patron Elder Gods, such as is the case with the Great Fairies of Power, Courage, Wisdom, and Wind.
Great Fairy of Magic
Second only to the High Queen of Fairies, the Great Fairy of Magic is an immensely powerful being in her own right, and may in fact be a Fairy Queen.
Guardian Fairy
A Sprite dedicated to guarding or guiding a specific individual: most often Kokiri, although mortal children occasionally receive a guardian. A Sprite may give odd bits of advice (always to be heeded) to adults, but cannot or will not adopt one.
High Queen of Fairies
Tremendously powerful, she is believed by some to be the personification of Fortune or the Fates, the High Queen of Fairies takes three forms: a beautiful young woman or child, a regal woman, or an old crone. Those who manage to find her, or more likely, stumble across her, will meet their fortunes whether good or ill. She has been known to favour the Great Heroes. All other fairies answer to her. If she has a name, she has yet to part with it.
Mayfly (Spirit of Truth)
A Virtue, she gives blessings to those who show honesty.
Selki (Queen of the Seas)
A lesser Fairy Queen, Selki is the most powerful of the sea born fairies, and thought to be the wife of Oshus.
Venus (Queen of Happiness)
A fairy queen, Venus appears in springtime as a beautiful maiden. She bestows gifts on those who prove themselves worthy.
OTHER
Fierce Deity
A god of war, the Fierce Deity was sealed into a mask, his power is feared and revered, used with caution in times of strife.
Hero of Time
Said to be a disciple of Time, the Hero of Time and Masks may have ascended on his own power, or that of the Fierce Deity, or by the force of belief in him from generations of mortals – both before and after his time. He is the model Hero all after him strive to follow.
Hero's Shade (Golden Wolf)
The spirit of an old Hero, he carries regret, although why for, no one knows. Did he fail in some task, or leave something undone? Or does he watch over his descendants, or wish to atone for a long forgotten misdeed? None know: he has never been known to speak. He is thought to travel the realms of Hyrule as a one-eyed wolf, warning of danger and guiding lost travellers in far off places.
Kaepora Gaebora
Said to be the reincarnation of an ancient, now ascended sage, the great horned owl Kaepora Gaebora is a protector of children and guide to travellers. He is known to favour Heroes, and for vanity – it is said as a mortal he was either a singer, public speaker, or a teacher: whichever is the case he seems to love the sound of his own voice.
Phi or Fi
A largely forgotten spirit, little is known of Phi, only that she does have influence on mortal affairs. Some say she is the spirit of the Master Sword, who chooses those worthy of the blade. Others say she once resided in the sword but after taking into herself the Gods' gifts grew powerful and locked Demise away with herself in eternal combat, never to harm the world again.
Sacred Beast (The Wolf)
Believed to be the Hero of Twilight, who must have ascended in order to have slain the avatar of Mawt, the Sacred Beast is a protector of animals and travellers, a patron to subsequent heroes, and, oddly enough, haberdashers. He is associated with the Golden Wolf, who is said to be his ancestor.
Spirits of Season
The personifications and protector deities of the four seasons, the Season Spirits often appear in the wilds of Holodrum. They resemble fairies, and occasionally deign to answer to the High Queen, but are not in fact Fay.
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Next up, Of Ganon