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In the Guard house with all of the pots, crash into one of the crates
On the side of the gate outside of the castle(adult)
Roll into the tree right as soon as you enter the Hyrule castle stage
Play the Song of Storms right next to the tree that in just inside the castle gate

Kokiri Village

The magic bean hole right next to the Shop
Behind the Know-It-All Brothers hut
On top of the house that is closest to the entrance to the deku tree

Lost Woods

The magic bean hole that is on the side of the cliff at the entrance to Kokiri Village if you were going to come in from Hyrule Field
In the Sacred Forest Area, when you are on top of the hedges, look around

Karkario Village

The magic bean hole in the Graveyard
If you just enter the graveyard it is on the right side wall and to the back
On the look out tower on the ladder
On the side of the House with the metal roof
On top of the house with the Cow inside
Roll into the tree where the monster child is
On the side of the Skulltula House

Death Mountain

In the first Cave that has a diamond on the front
Behind the boulder where the bomb flower is(adult)
Right before the wall with all the regular spiders on it and after the falling rocks have stopped(adult)

Death Mountain Crater

The magic bean hole right outside of the Fire Temple
In the crate at the entrance(child)

Goron City

In the crate at the end on the boulder maze room
On the back of the platform that used to have the Fire Spiritual Stone in it

Zora's River

Roll into the tree that is right at the entrance to the area if you are coming from the Hyrule Field
Climb the ladder and turn 180 degrees and jump over the other platform. There should be one right off to the side
Towards the end of the river, if you can in from the Hyrule Field, on the bridge, look up

Zora's Domain

At the top of the waterfall, look to the left(adult)

Jabu-Jabu's Fountain

At the end of the fallen log, look at the wall
Roll into the tree at the entrance to the Great Fairy's Cave
Life the boulder in front of the Great Fairy's Cave to discover a passageway. Use the Lens of Truth to see the spiders and at the end is the skulltula(adult)

Hyrule Field

Near the entrance to the Gerudo Valley, there is a boulder with a small passage beneath it
On the side of the castle, near the entrance to Karkario Village is a tree that you bomb a hole next to to discover a cave

Lake Hyrule

The Magic Bean Hole right outside of the Lake Laboratory
On the Back of the Lake Laboratory(Child)
At the bottom of the Lake Laboratory in the crate
On the Island where you get the Fire Arrows(child)
On top of the tree on the island(adult)

Gerudo Valley

The magic bean hole at the bottom of the valley
As you walk in, look at the waterfall
Behind the Carpenter's tent(adult)

Gerudo Fortress

On the top level, in the middle, outside(don't know how else to explain it)
On the target to the farthest left when you just enter the Archery Range

Haunted Wasteland

Inside the building, down the ladder, that you use the Lens of Truth to see in ghost
On the tree next to the dried up lake
The magic bean hole right next to the Entrance to the Spirit Temple
Take the magic bean at night and you will see one on a sand mound, just jump down onto it

Cursed Spider Prizes

10 spiders : Adult wallet - Hold up to 200 rupees
20 spiders : Stone of Agony - Rumbles when there is a secret in the room
30 spiders : Gaint's wallet - Hold up to 500 ruppees
40 spiders : Bombachu - Mobile bomb
50 spiders : Peice of Heart - Get 4 to get a heart container

Can't find the Skulltula here? Click Here.