The present invention relates to a pharmaceutical composition for the prevention or treatment of diseases mediated by excessive histamine comprising naturally-derived isoorientin, a use of isoorientin for the manufacture of a medicament for the prevention or treatment of diseases mediated by excessive histamine, and a method for preventing or treating diseases mediated by excessive histamine comprising administering a therapeutically effective amount of isoorientin to a subject. The composition, use and method of the present invention show excellent histamine suppression effects, and so can be used for the prevention or treatment of various kinds of allergic disease, atopic disease, inflammatory disease, skin disease, hyperacidity and nervous system disorder.