A comparative analysis of cotranscribed gene clusters comprising the structural genesmcrA,mcrB,mcrC,mcrD, andmcrG was carried out in three species of methanogens.mcrA,mcrB, andmcrG are the structural genes for the three subunits of methyl coenzyme M reductase, while the two other genes encode polypeptides of unknown functions. The degree of conservation of themcrgene products among different species of methanogens varies. No correlation was found between the conservation of the G + C contents of the homologous genes and of the amino acid sequences of their products among the different bacteria. The comparison of RNA polymerase core subunit genes ofMethanobacterium thermoautotrophicumas evolutionary markers with their equivalents inEscherichia coli,Saccharomyces cerevisiae, andDrosophila melanogastershowed that homologous polypeptide domains are encoded by different numbers of genes suggesting gene fusion of adjacent genes in the course of evolution. The archaebacterial subunits exhibit much stronger homology with their eukaryotic than with their eubacterial equivalents on the polypeptide sequence level. All the analyzed genes are preceded by ribosome binding sites of eubacterial type. In addition to known putative promoter sequences, conserved structural elements of the DNA were detected surrounding the transcription initiation sites of themcrgenes.Key words: archaebacteria, methanogens, gene structure, RNA polymerase, promoter.