AGA and AGG (AGR) are arginine codons in the universal genetic code. These codons are read as serine or are used as stop codons in metazoan mitochondria. The arginine residues coded by AGR in yeast or Trypanosoma are coded by arginine CGN throughout metazoan mitochondria. AGR serine sites in metazoan mitochondria are occupied mainly in corresponding sites in yeast or Trypanosoma mitochondria by UCN serine, AGY serine, or codons for amino acids other than serine or arginine. Based on these observations, we propose the following evolutionary events. AGR codons became unassigned because of deletion of tRNA Arg (UCU) and elimination of AGR codons by conversion to CGN arginine codons. Upon acquisition by serine tRNA of pairing ability with AGR codons, some codons for amino acids other than arginine mutated to AGR, and were captured by anticodon GCU in serine tRNA. During vertebrate mitochondrial evolution, AGR stop codons presumably were created from UAG stop by deletion of the first nucleotide U and by use of R as the third nucleotide that had existed next to the ancestral UAG stop.