Back in this room, look directly across at the golden eye switch . Shoot it with your Hero’s Bow to cause the middle platform become to rise up and down. Use the Deku Flower here to fly to the middle platform, then across and into the Gekko Room.
A Gekko is in this room and must be defeated. Hit it three times and it will summon a Snapper. The Gekko leaps onto the Snapper and starts whirling around the room, you need to use a Bomb or the Deku Flower to flip the Snapper.
At this time the Gekko will crawl around the walls, shoot it with an arrow and the sequence repeats. Do this three times to defeat the Gekko and gain access to the chest behind the door which has the Boss Key .