A 5.7 kb region of chromosomal DNA from Methanothermus fervidus, harbouring a second mcr gene cluster, was cloned and sequenced. This gene cluster, termed mcrII, encodes an isoenzyme of methyl coenzyme M reductase (MCR). In contrast to the known mcr gene clusters from other methanogens, mcrII lacks mcrC, a gene of unknown function. But the remaining mcrII genes B, D, G and A are arranged in the same order as in previously sequenced mcr gene clusters. The mcrII genes from M. fervidus are located 3' to the open reading frame (ORF) B of the methylviologen-reducing hydrogenase (mvh) gene cluster. The genes of mcrII are cotranscribed, resulting in an mRNA of 4500 nucleotides. The transcriptional initiation and termination sites were identified. Phylogenetic reconstructions reveal that the mcr gene clusters fall into two different types, I and II, and that the ancestral mcr gene cluster was duplicated before the segregation of methanogens into three major orders occurred.