Impact statement For decades, Thermus was always considered to be aerobic. However, recent studies have suggested that the denitrification abilities of Thermus species may be widely underestimated. In the present study, we used comparative genomic analysis to investigate the evolutionary history of the denitrification pathway in Thermus and other members of the phylum Deinococcota . We revealed incomplete denitrification pathways to be common in Thermus and showed they are inherited mostly vertically, which further supports the importance of Thermus as a significant denitrifier in hydrothermal environments.