The present invention provides a method for transforming organelles having an own genomic DNA, the method enabling efficient production of highly homoplasmic plant cells, in which most of the organelles are transformed, and so forth. The method comprises the steps of: expressing in plant cells a fusion protein containing a function inhibiting factor of the organelles and a transit signal peptide to the organelles introducing into the genomic DNA of the organelles of the plant cells an expression cassette comprising DNAs encoding a restoring factor of the organelles and a factor desired to be expressed in the organelles and allowing the function inhibiting factor to destroy the organelles, in which the expression cassette is not introduced, in the plant cells.
