The phylogenetic placement of Thermodesulfovibrio yellowstonii was investigated on the basis of gene order data from completely sequenced bacterial genomes. T. yellowstonii was found to share four gene arrangements characteristic of the Proteobacteria, Aquificae, Planctomycetes, Spirochaetes, Bacteroidetes, Chlorobi, Acidobacteria, Verrucomicrobia and termite group 1, the presence of which defines superphylum 2. The remaining phyla show sets of alternative gene arrangements and form superphylum 1. An analysis of conserved gene pairs showed that the overall genome organization of T. yellowstonii is most similar to that of deltaproteobacteria. Three arrangements that suggest gene translocations were identified that are likely to have occurred in a common ancestor of T. yellowstonii and the Proteobacteria exclusive of virtually all other major bacterial phyla. The translocation events suggest the closest evolutionary relationship between T. yellowstonii and the Proteobacteria.