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I will split this section into two parts, ones you can get as Young Link, and Adult Link. All the ones that you can get as both will be put on the Young Link section. I hope this section can help you out. A reminder some of the tokens can only be collected with the Boomerang or the Longshot, I will not write down which ones are like that. Tip: Listen for the scraching noises.
20 Gold Skulltulas Killed-Stone of Agony
30 Gold Skulltulas Killed-Giants Wallet (holds 500 rupees)
40 Gold Skulltulas Killed-Bombchu
50 Gold Skulltulas Killed-Piece of Heart
100 Gold Skulltulas Killed-Gold Rupee (200 rupees)
1. At night behind the Know-It-All brother's house.
2. Drop a bug in the soil spot beside the Kokiri Shop.
3. In the room with the three rising pilers, there is one in the left area.
4. In the basement there is one on the bars in the water.
5. There is on the vines that you use to climb back up to the first floor.
6. In the room with three baby Gohmas there is a bombable wall, bomb it and go in.
8. In the circle of stones just outside of Geruodo valley, place a bomb there and go in pit.
9. In the room with all the pots, there is one in a crate.
10. Play the song of storms infront of the tree by the corner where you meet Talon.
11. Roll in the tree that is by that guard guarding the castle entrance.
13. At night there is a Skulltula on the back of that wooden part of the circle with all the horses.
14. At night on the outer wall on Links North east (when he is entering).
15. At night there is one on the second storey window of Talon's house.
17. At night on the side of the House of Skulltula.
18. At night there is one on a pile of bricks at the house under construction.
19. At night on the side of the house of the kid in the graveyard.
20. At night there is one on the lookout tower's ladder.
22. Drop a bug into the bean hole.
24. Drop a bug into the bean hole infront of Dodongo's Cavern.
27. Drop a bug in the bean hole by the two buisness Scrubs.
29. In the room with the stairs that come down, at the top of the stairs there is a Skulltula (might be easier to use longshot).
30. In the same room as above, there is a Skulltula and a Gold Skulltula on some vines.
31. In the room you have to go to push that block there's a bombable wall, bomb it and go in there.
33. Roll into the tree at the beggining of the river.
35. At night, there is one behind the fallen trees on the wall.
37. At night there is one on the side of the Lakeside Laboritory.
38. Drop a bug into the bean hole beside the Lakeside Laboritory.
40. In the room where the Princess falls to, there is one on the outer wall.
41. In the room with the little water that you can change the water level, there is one on the wall.
42. In the room just before Barinade, there is one on some vines.
44. Warp to the crate using your song and drop bugs into the bean hole.
46. A bean hole under the bridge housed a Gold Skulltula.
49. There is a Gold Skulltula on by the wall you use to climb to the second floor.
50. In the room just before Iron Knuckle there is a Gold Skulltulla.
52. In the room with the compass there is a room on the left side with chains, there is one in there (use lens of truth to get to it).
53. In the room with the thing that sucks off your speical equipment, there is one behind it.
58. When you get onto the ledge with the Deku Baba there is one on the wall to the left.
59. In the room just before the falling roof, there is one on the wall.
60. In the room with the four torches, there is one on the right side if you go straight.
61. In the room just before Phantom Ganondorf with the movable walls, there is one in one of the rooms.
64. Near Biggoron there are three rocks, use the hammer to break them and begin the last on is a Gold Skulltula.
67. In the room with the spining tiles there is one behind the thing that sucks off your spiecal equipment.
68. In the room with the rolling Gorons there is a wall that makes a scraching sound, bomb it.
69. On the chain wall that leads to the gold rupee the is one on the chain wall.
70. In the room with the gold rupee there is a gold skulltula on the wall.
72. At night there is one on the wall near the bridge.
76. In the room with the compass there is a Gold Skulltula.
77. In the final room where you have to collect the silver rupees there is a Gold Skulltula.
79. At night there is one on top of the tree on the island with the saying about the fire arrows.
81. In the room with the iron bars and the dimond shaped thing there is one behind it (use spin attack to open).
82. In the room with the waterfall and those things falling, there is one on the right wall.
83. In the river with all the vortexs' there is one on the left wall (use iron boots and longshot to get it).
84. In the room with the rolling Gorons the is a little waterfall with a Gold Skulltula on it.
86. In the room with the falling spears there is one in a barred room.
87. In the room with the statue with the blue thing coming out, there is one behind it.
88. By the ship, play the scarcrows song and longshot onto Peirre and there is one by him.
89. In the room with the three statues with the blue stuff coming out, there is a Gold Skulltula on the wall.
91. At night there is one on the stone arch.
93. At night there is one on one of the targets at the Archery Game.
96. At night there is one on a platform that you can get using the Magic Bean.
98. Just before entering to get to Twinrova there is one on the left wall.
