Thorns on citrus trees develop at the nodes, often sprouting on new grafts and fruiting wood. Some citrus trees with thorns outgrow them as the tree matures. The presence of thorns on citrus trees has evolved for exactly the same reason that animals such as hedgehogs and porcupines sport prickly hides– protection from predators, specifically, hungry animals that want to nibble away at the tender leaves and fruit. Vegetation is most delicate when the tree is young. For this reason, while many juvenile citrus have thorns, mature specimens often do not.
While many citrus trees grow thorns at some point during their life cycle, pruning them away will not damage the tree. Mature trees usually grow thorns less frequently than newly grafted trees that still have tender foliage needing protection. Fruit growers who graft trees should remove thorns from the rootstock when grafting. Most other casual gardeners can safely prune the thorns for safety’s sake without fear of damaging the tree.
This may be coming from your root stock. An orange tree is actually two different varieties that have been grafted together to form one tree: The rootstock is selected for its hardiness and resistance to disease, while the upper part, or scion, is chosen for its desirable fruit. Orange trees do not require a great deal of pruning but the removal of suckers is essential for proper care and health of the tree. Suckers are branches that sprout from the rootstock below the graft union. If allowed to develop, these suckers will rob the strength from the upper part of the tree, eventually affecting the tree's ability to produce the preferred variety of orange. Suckers should be removed as soon as possible before they become established, regardless of the season.
Identify the graft union on the orange tree. The graft union is a diagonal scar approximately 6 to 12 inches above the ground, depending on the age and size of the tree. The trunk below the graft union may have a different color bark than above the graft union. Branches from the rootstock may have a different type of leaf than the branches from the scion.
Use your fingers to snap off any green branches below the orange tree's graft union. Remove the suckers as close as possible to the trunk of the tree. Do not tear the bark of the tree's trunk.
Use sharp, sterile bypass pruners to remove suckers up to 3/4 inch in diameter that have developed woody tissue. Make a clean, vertical cut as close as possible to the trunk of the tree, without damaging the branch collar, the ring that forms on the trunk around a branch. Bypass loppers should be used on larger woody branches up to 1 3/4 inches in diameter, while pruning saws are used for branches up to 2 1/2 inches in diameter.