Nayru’s Pearl is the third and last of three pearls that Link has to obtain in The Wind Waker. This pearl is initially owned by Jabun of Greatfish Isle. However, when Link travels to the isle, he finds that it has been destroyed by Ganondorf.10 Fortunately, Jabun sensed him coming and fled to Outset Island. Link and the King of Red Lions travel to his cave after the stone door is broken down by Link using the cannon and bombs. Jabun, after some convincing from the King of Red Lions, then gives the pearl to Link. Link then places the pearl on Southern Triangle Island to raise the Tower of the Gods from beneath the Great Sea.
Nayru’s Pearl has the same mark on it as the symbol for the Tune of Ages from Oracle of Ages and as the Wisdom Gem. It also appears on a door inside the Temple of the Ocean King – Zelda Wiki