Plastids (including chloroplasts) and mitochondria are remnants of endosymbiotic bacteria yet maintain their own genomes, which encode vital components for photosynthesis and respiration, respectively. Organellar genomes have distinctive features, such as being present as multicopies, being mostly inherited maternally, having characteristic genomic structures, and undergoing frequent homologous recombination. To date, it has proven challenging to modify these genomes. For example, while CRISPR/Cas9 is a widely used system for editing nuclear genes, it has not yet been successfully applied to organellar genomes. Recently, however, precise gene editing technologies have been successfully applied to organellar genomes. Protein-based enzymes, especially TALENs and artificial enzymes utilizing TALEs, have been successfully used to modify these genomes by harnessing organellar targeting signals. This short review introduces and discusses the use of targeted nucleases and base editors on organellar genomes, their effects, and their potential applications in plant science and breeding.