Because small subunit ribosomal RNA sequences are the standard for defining the phylogenetic positions of organisms, a large data base of ribosomal RNAs exists and one knows far more about the organization of ribosomal operons than about any other operons. Eubacteria, halobacteria, methanogens, and eocytes contain three rRNAs, 16S, 23S, and 5S, which are homologous to the eukaryotic 18S, 5.8S+28S, and 5S. (For simplicity we will refer to both the eukaryotic and prokaryotic homologues using the prokaryotic labels.) The number of ribosomal rRNA transcriptional units varies between one and four in the halobacteria and the methanogens. Ribosomal operons are arranged in the same general pattern in eubacteria, halobacteria, and methanogens, namely 16S-tRNA-23S-5S. Occasionally an additional tRNA gene will be found between the 16S and 23S genes or following the 5S gene (reviewed in Brown, Daniels, & Reeve, 1989). Thermoplasma, which routinely clusters in phylogenetic trees with the methanogens, is an exception to this general rule and unlike any other prokaryote. Thermoplasma contains unlinked 16S, 23S and 5S genes (Tu & Zillig, 1982). The pattern in eocytes and eukaryotes is different from the eubacteria, halobacteria, and methanogens. In the eocytes, the 16S-23S genes are linked without a tRNA spacer and there is a variable linkage of 5S rRNA encoding genes to the 16S-23S unit. The non-operon-associated 5S rRNA gene of D. mobilis forms its own transcriptional unit (Kjems & Garrett, 1988), but those of many other eocytes contain a 16S-23S-5S transcriptional unit. The eukaryotic pattern is similar with a 16S-23S (equivalent) transcription unit lacking tRNA spacers and with the 5S either separately transcribed or linked (Gerbi, 1985). An exception to this rule is found among the Cryptomonads where the rRNA genes are unlinked (Gray, 1992).