Protoplast fusion can overcome the sexual incompatibility barriers that exist between different plant species and can give rise to novel plants that cannot be produced in nature. It therefore provides a new source of genetic variation, particularly within the cytoplasmic organelles. We review the mixtures, rearrangements, and recombinations of mitochondrial and chloroplast genomes in plants regenerated from protoplast fusion products. Particular emphasis is placed on canola fusion systems that are being utilized in the commercial production of hybrid seed for a worldwide market.