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The present disclosure provides biophotonic compositions containing halogen ions and/or halogen salts and methods useful in phototherapy. In particular, the biophotonic compositions comprising halogen of the present disclosure include at least one chromophore; and halogens and/or halogen salts such KI, or KCl, or KBr, or CsBr, or MgBr2, or ZnBr2, or NaF, or NaCl, or NaBr, or I2, or I3−, or Br2, or Cl2. The biophotonic compositions and the methods of the present disclosure are useful for promoting tissue repair, wound healing, bone regeneration and skin rejuvenation, as well as treating oral diseases, microbial and viral infections, acne and various other skin disorders and various orphan diseases.