The present invention relates to a composition for preventing at least one plant disease resulted from infection of plant pathogens and a method for preparing the same. Particularly, the composition contains extract of at least one plant selected from the group consisting of Coptis chinensis Franch., Phellodendron genus plant, Sanguinaria canadensis and Chelidonium majus var. asiaticum which are natural plants having anti-plant pathogen activity or berberine which is purified therefrom. The composition of the present invention can be effectively used for preventing disease pathogens such as plant powdery mildew, anthracnose of pepper, damping-off of cucumber and gray mold rot of strawberry resulted from infection of plant pathogens such as Colletrotrichum gloeosporiodes, Pythium ultimum or Botrytis cinerea. For an alternative method for preparing the composition comprising berberine and/or derivatives thereof, the present invention provides various optimal culture condition and two phases cultivation methods using Phellodendron genus plant.