A method for inducing a structural change in a plant mitochondrial genome is provided. The invention relates to a method for inducing a structural change in a mitochondrial genome in a plant cell by introducing a double-strand break into a target sequence region on mitochondrial genomic DNA in a plant cell, which is present in individual molecule species of the mitochondrial genomic DNA. In addition, the present invention also relates to a method for deleting a gene that is present in mitochondrial genomic DNA in a plant cell by introducing a double-strand break into the gene or a region near the gene, which is present in individual molecule species of the mitochondrial genomic DNA. Moreover, the invention also relates to a plant cell having a mitochondrial genome, in which a structural change has been induced by the method, and a seed and a plant having the plant cell.
