Magic roots are the roots of the magic tree which is obtained with the Farming skill. Players with level 75 farming may plant a magic seed in a tree patch.
Once the tree has grown, the player may use an axe to chop the tree down to a stump, and then use a spade on the stump to dig up the tree roots, clearing the patch for another tree, and putting the magic root into the farmer's inventory.
If the roots are not immediately dug up, the tree will respawn and it may be cut down again. Multiple roots can be obtained at higher farming levels. 1 root is obtained at 75, 2 at 83, 3 at 91, and 4 at 99.
Obtaining at least 3 magic roots when digging up a magic tree stump is an elite task in the Falador Diary.
As with all tree roots, magic roots may be used in a compost bin to make supercompost. However, magic roots may be spun into magic string (instead of crossbow string like other roots) by using the magic roots on a spinning wheel, with level 19 Crafting. Magic roots are also a component in the Herblore skill to make Antidote++.
For an exhaustive list of all known sources for this item, see here