The present invention provides a fungicidal composition comprising a strain of Bacillus subtilis or Bacillus amyloliquefaciens and one of several compounds in a synergistically effective amount. Also provided are methods of controlling fungal harmful organisms and/or bacterial harmful organisms in a plant, the method comprising applying an effective amount of a fungicidal composition to the plant, to a part of the plant and/or to a locus on which the plant or plant part grows.