The complete nucleotide sequence of the 16S rRNA gene from Thermoplasma acidophilum, as well as its 5' and 3' flanking regions, were determined by the dideoxynucleotide chain termination method. The 16S rRNA gene encodes 1471 nucleotides. The primary and secondary structures of T. acidophilum 16S rRNA both exhibit typical archaebacterial features. The sequence appears to be more closely related to 16S rRNAs of the methanogen--halophile group than to those of the thermoacidophile group. Secondary-structure comparisons generally support this relationship, although there are several examples in which the single-stranded loops in particular helices of T. acidophilum 16S rRNA more strongly resemble their counterparts in the 16S rRNA of Sulfolobus solfataricus, a member of the thermoacidophile group. In contrast to the polycistronic rRNA operons found in most organisms, the three rRNA genes from T. acidophilum occur in only a single copy per genome and appear to be physically unlinked. Consistent with this, the 16S rRNA gene is flanked by putative promoter and terminator sequences that are comparable to the transcription control signals from other archaebacterial genes. The sequence TATATATA, which is very similar to the archaebacterial promoter consensus TTTAT/AATA, is located 18 bases before the probable site of transcription initiation, TGCACAT. There is a potential transcription termination site immediately downstream from the gene that consists of a relatively stable stem and loop structure followed by stretches of Tresidues.