RNA editing converts many specific C residues into U residues in plant organelles. Recently, a pentatricopeptide repeat (PPR) protein was shown to be required for RNA editing site recognition as a trans-factor. Many PPR proteins recognize multiple sequences surrounding the target C residues (cis-elements), which are often not highly conserved. Based on the accumulating information on trans-factors, it is possible to discuss their co-evolution with RNA editing sites. One surprising discovery is that plants edit many sites, even when the resulting amino acid changes are not required for their protein function (functionally silent editing). Thus, it is unlikely that RNA editing is simply a process correcting the T-to-C mutations in the genome at the level of RNA. In this review article, I discuss the possibility that RNA editing is the evolutional system that promotes the evolution of genes encoded by organelle genomes.