RNA editing converts hundreds of cytidines into uridines in plant mitochondrial and chloroplast transcripts. Recognition of the RNA editing sites in the organelle transcriptomes requires numerous specific, nuclear-encoded RNA-binding pentatricopeptide repeat (PPR) proteins with characteristic carboxy-terminal protein domain extensions (E/DYW) previously thought to be unique to plants. However, a small gene family of such plant-like PPR proteins of the DYW-type was recently discovered in the genome of the protist Naegleria gruberi. This raised the possibility that plant-like RNA editing may occur in this amoeboflagellate. Accordingly, we have investigated the mitochondrial transcriptome of Naegleria gruberi and here report on identification of two sites of C-to-U RNA editing in the cox1 gene and in the cox3 gene, both of which reconstitute amino acid codon identities highly conserved in evolution. An estimated 1.5 billion years of evolution separate the heterolobosean protist Naegleria from the plant lineage. The new findings either suggest horizontal gene transfer of RNA editing factors or that plant-type RNA editing is evolutionarily much more ancestral than previously thought and yet to be discovered in many other ancient eukaryotic lineages.