
The Tree of Harmony is a magical tree that holds the Elements of Harmony. It is located in the Everfree Forest, near Princess Celestia and Princess Luna's old castle. The center of the tree has a star shaped like Twilight Sparkle's cutie mark, while Celestia and Luna's cutie marks are on the trunk.
Depiction in the series
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Princess Twilight Sparkle - Part 2
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According to Celestia, the tree controls and contains all that grows in the Everfree Forest, even without the Elements in it.
Twilight Sparkle and her friends discover that the Tree of Harmony has lost its magic, allowing Discord's plunderseeds to sprout and grow all over the Everfree Forest, slowly killing the tree. Twilight and her friends give up the Elements of Harmony and return them to the tree, recharging its magic and restoring the forest.

The mysterious chest.
Twilight's Kingdom - Part 2
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The tree is seen again with the Elements of Harmony still on its branches with the mysterious chest in front of it. At the episode's climax, the tree activates the elements and connects them with the rainbow power that came from the chest. The tree then transports the chest into the ground in Ponyville, which sprouts into Twilight's new castle. The new castle partly resembles the tree itself.
Season five
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The tree is mentioned by Rainbow Dash in The Cutie Map - Part 1, giving Twilight an example on what else is there left to do.
Twilight also mentions the tree in The Cutie Re-Mark - Part 1, surmising that its connection to the Cutie Map explains its presence even after the timeline is altered.
Other depictions
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In The Journal of the Two Sisters, Star Swirl the Bearded show a young Luna and Celestia the tree. The tree had the three cutie marks before Celestia and Luna received theirs. It is implied that Star Swirl knew that Twilight was going to get the third cutie mark.
The tree is used in Gameloft's mobile game.