SignificanceIn this work, we provide compelling evidence thatEuplotesgenetic code violates the triplet nature of the genetic decoding that was thought to be universal. Thus,Euplotespossess the most extreme example of genetic code variation described so far. The nontriplecy arises from abundant ribosomal frameshift sites with no regulatory function, where stop-codons distant from the 3′ transcript end specify +1 or +2 ribosomal frameshifting with high accuracy. We show that this violation of the triplet coding inEuplotesis brought about and further maintained by neutral evolution rather than selective processes but still is irreversible.