Inside the Deku Tree
Young Link
1. In a crate next to the treasure chest that contains the map. (1st floor)
2. Use a bombchu to blow up the rocks at the top of the wall that you can climb in the room where the compass is located. (2nd floor)
3. Play the Song of Time continuously in the room with four torches to create a stairway to the ceiling. (Basement 1)
4. Head to the small room adjacent to the room where the previous Gold Skulltula is located. (Basement 1)

Dodongo's Cavern
Young or Adult Link
1. In the room adjacent to the room with the Bomb Flowers surrounding the staircase there are many blue blocks. Use the Song of Time to clear away the block in the far left corner of the room. (1st floor)
2. In the room adjacent to the room where you have to move three blocks to light three torches there is a Gold Skulltula in a crate on the right. (2nd floor)
3. Blow up the rocks blocking the path in the first room where you fight Lizalfos'. (2nd floor)
4. In the room adjacent to the one just before you reach the treasure chest that contains the bomb bag, use the boomerang to reach the Gold Skulltula in the upper left corner. (1st floor)
5. Stand in front of the door (near the Armos') at the far end of the room with three tombstones. The Gold Skulltula is just barely visible on the ledge. (1st floor)

Inside Jabu-Jabu's Belly
Young Link
1. In the room adjacent to the room where you pick up Ruto defeat all the enemies (there are some invisible Keese, so consider getting the Lens of Truth before doing this). Use the target that appears to climb onto the ledge. (Basement 1)
2. Use the Song of Time to move the blue block in the room where you find the boomerang. (Basement 1)
3. In the room with three hallways, take the left hallway, then go through the right door. Use a bombchu to blow up the rock near the ceiling. (1st floor)
4. In the room before Barinade, climb up onto the high ledge and use the boomerang to hit the Skulltula behind the glass. (1st floor)