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One of the toughest challenges in this game is finding all them Gold Skulltulas. Well, to make it easy on anyone who still don't know where they are, here's all of their locations

Kokiri Forest

Behind the Know it all Brothers House Young Link
Behind the Twins' house Adult Link
Drop a bug in the bean hole to sprout one Young Link

Great Deku Tree

In a small crevice on the third floor Any Age
In the hole where you fall through in the beginning, there's one on the vines Any Age
In that same room on the left, there's one on the grate Any Age
Through the crawl space there's a wall to be bombed. Inside is another skulltula Any Age

Lost Woods

From where you enter, go left twice and plant a bug in the bean hole Young Link
From where you enter, go left, right, left, right, left, left and plant another bug in the bean hole Young Link
Go to the same place where you planted the second bug in the beanhole. The stalk will take you up to another skulltula Adult Link
From the sacred meadow, go down the large stair, up the ladder, and look to the left wall. There should be a skulltula there Adult Link

Hyrule Field

In a tree to the right of Hyrule Castle Any Age
In the stone circle near the Gerudo Valley entrance Any Age

Hyrule Castle

When you first enter, go into the room on the right. Smash all the boxes and inside one of them is a skulltula Young Link
Play the Song of Storms near a tree at the castles entrance Young Link
In the tree where the owl was sitting in front of the castle gate Young Link
Near Ganon's Tower under the stone arch Adult Link

Lon Lon Ranch

When you approach the field where the horses are, go left and slam into the tree Young Link
Behind the corral Young Link
Just northeast of where you got that last one, there's one on the wall Young Link
On the second floor window of Talon's House Young Link

Kakariko Village

Slam into the tree just outside the entrance to Kakariko Village (It's really in Hyrule Field) Young Link
Behind the House of Skulltula Young Link
Where the construction is going on, there's one on top of the bricks Young Link
In the graveyard, there's one high up on the northeast wall Younk Link
On the ladder of the lookout tower Young Link
On top of Impa's House (the one where the owl takes you when you're young) Adult Link
Plant a bug in the bean hole in the graveyard Adult Link

Goron City

Behind all the rocks in one of the rooms Adult Link
On the central platform Adult Link

Dodongo's Cavern

Behind a bombable wall where the baby dodongo's are Any Age
In that same room, use the scarecrow song and the hookshot to reach another one Adult Link
In the room with the BIG staircase, inside a little crevice in the wall Any Age
Also in that room there's one on the vines Any Age
In a room near the boss, there's a bombable wall (the on with the all the blocks) Any Age

Death Mountain

Plant a bug in the bean hole outside Dodongo's Cavern Young Link
Smash the rock on the ledge above Dodongo's Cavern Adult Link
Smash the rock on the right wall where the falling rocks are Adult Link
Bomb the wall on the right when first entering Death Mountain Any Age

Lake Hylia

On the little island where you get the fire arrow Young Link
At the bottom of the Laboratory's diving tank in a crate Adult Link
Behind the Laboratory Young Link
On top of the large dead tree above the Water Temple Adult Link
Plant a bug in the bean hole near the Laboratory Young Link

Zora's River

On the little ladder just outside the entrance to Zora's Lair Young Link
Slam into the tree at the entrance to the river Young Link
High on a wall. Go up the ladder to the top of that high ledge near where you get the piece of heart. Look to the wall on the left Adult Link
Just above the bridge high on the wall Adult Link

Zora's Domain

At the top of the frozen waterfall Adult Link

Zora's Fountain

Smash into the tree on the southeast corner Young Link
To the right of the fallen log Young Link
Under a rock near the Great Fairy, there's a secret cave. At the end you'll find a skulltula Adult Link

Jabu Jabu's Belly

Look at the vines in the room where you raise the water Young Link
Look within the holes of Jabu Jabu Young Link
On the vines in the room just before the boss Young Link
On one of the basement walls Young Link
Another one on the basement walls just before Big Octo's room Young Link
Another on a rough wall before the bosses room Young Link
Another in the belly area of Jabu Jabu Young Link

Death Mountain Crater

Plant a bug in the bean hole outside of the Fire Temple Young Link
In a crate near the entrance Adult Link

Forest Temple

On the vines in the first room Adult Link
On the wall near the door in the main room opposite the entrance Adult Link
The east plant room near the chest Adult Link
The west plant room on a balcony Adult Link
In the rotating room near the boss Adult Link

Ice Cavern

In the room where you find the piece of heart Adult Link
On a wall in the ice block room Adult Link
In the room with the giant ice scythe Adult Link

Fire Temple

West side of the room with the bridge. Play the song of time Adult Link
In the maze room, look for a bombable floor Adult Link
In the room with the shield eater Adult Link
On the second floor, look for a high platform and play the scarecrow song Adult Link
On the left wall in the room where the hammer is Adult Link

Water Temple

In a room behind where the boulders fall on the left Adult Link
Use your spin attack to get the one in the basement cell Adult Link
On the wall where the two water falls are Adult Link
On top of the central tower Adult Link
On a wall near the wirlpool Adult Link

Gerudo Valley

On the right hand wall by the small log bridge Young Link
Behind the carpenters tent on a wall Adult Link
Under the large stone arch Adult Link
Plant a bug in the beanhole Young Link

Gerudo Fortress

High above the eastern wall of the fortress Adult Link
One the left most target at the archery area Adult Link

Bottom of the Well at Kakariko Village

In the cell with the like-like Young Link
In the room with the false floor Young Link
In the room with the Deku Plant Young Link

Haunted Wasteland

In the stone structure where the phantom lives Adult Link

Desert Collossus

There's one hiding in the palm trees Adult Link
Ride the magic bean stalk to find another Adult Link
Plant a bug in the beanhole Young Link

Spirit Temple

In the room with all the bats and the gate Young Link
On one of the rough walls Young Link
On a wall in the main chamber use the scarecrow song Adult Link
In the hallway leading to the mini-boss Young Link
In the boulder room, play the song of time Adult Link

Shadow Temple

In a room in basement 3 with the scythes Adult Link
In the room with the falling spike blocks Adult Link
In the room with the single vase Adult Link
In the room with three vases there's one Adult Link
There's another in the room with three vases you can get by playing the scarecrow song Adult Link

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