I ate a whole organic orange, skin and all and now I have bad hives. I can drink orange juice no problems. What is in the skin I'm allergic to?

The peel? Rarely, people may be allergic to an allergen present in the peel and not the "meat" of the fruit. If your have only reaction to organic orange, then one will need to consider what has been used to grow and treat the orange when grown "organically".