Mystery Seeds can be sprinkled on Owl Stones, yielding hints for the current dungeon or area. They can also be used on enemies to achieve a variety of effects, all of which are borrowed from the other obtainable seeds in the game.
Mystery Seeds are first found in Oracle of Seasons after the Rod of Seasons and the Power of Winter are retrieved from Subrosia. After returning from Subrosia, Link has the ability to freeze the water by changing the season to winter. Across the frozen water and through the forest a bit lie a Mystery Seed tree and an Owl Statue.
In Oracle of Ages, they are introduced by Queen Ambi, who sends Link on a quest to hunt for them. Once the Mystery Seeds are found in Deku Forest, they will return Link to Ambi's Palace, where he is rewarded with Bombs. Afterward, the tree is available to get more Mystery Seeds.