Sequence characterization of 16S rRNA has revealed an ancient divergence that divides prokaryotic organisms into eubacteria and archaebacteria1. This evolutionary split is so fundamental that by the 16S rRNA criterion, the archaebacteria appear to be as distinct from eubacteria as they are from eukaryotes2. Extensive comparison of the lipids3 and cell walls4,5 of the various archaebacterial species strongly supports this interpretation. Detailed molecular investigations of the archaebacteria have provided surprising findings concerning the RNA polymerases6,7, the translation system8,9, the rRNAs10 and the 5S rRNA11,12. Here we report the occurrence of a 231-nucleotide archaebacterial 5S rRNA homologue containing a 108-nucleotide segment in its interior that is not homologous to any region of a closely related normal-size 5S rRNA.