[4] The name of this phylum is derived from the existence of many of these organisms at high temperatures along with the characteristic sheath structure, or "toga", surrounding the cells of these species.

[3][11] A clade consisting of the deep-branching species Petrotoga mobilis, Kosmotoga olearia, and Thermotogales bacterium mesG1 was also supported by seven CSIs.

It is thought that this network helps to maintain ADP/ATP binding to the SecA protein at high temperatures, contributing to the overall thermostable phenotype some Thermotogales species.

[13] Athalassotoga Mesoaciditoga Marinitoga Tepiditoga Oceanotoga Geotoga Defluviitoga Petrotoga Kosmotoga Kosmotoga 2 Mesotoga Fervidobacterium Thermotoga Pseudothermotoga Thermosipho Athalassotoga Mesoaciditoga Mesotoga Kosmotoga Marinitoga Tepiditoga Oceanotoga Geotoga Defluviitoga Petrotoga Thermotoga Pseudothermotoga Fervidobacterium Thermosipho This phylum presently consists of a single class (Thermotogae), four orders (Thermotogales, Kosmotogales, Petrotogales, and Mesoaciditogales) and five families (Thermatogaceae, Fervidobacteriaceae, Kosmotogaceae, Petrotogaceae, and Mesoaciditogaceae).

[2][5] However, a close relationship of the Thermotogota to the Aquificota, and the deep branching of the latter group of species, is not supported by phylogenetic studies based upon other gene/protein sequences.

[31][32][11][33] The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN)[34] and National Center for Biotechnology Information (NCBI)[35]