The presence of an A/V-type ATPase in different Thermus species and in the deeper branching species Meiothermus ruber and Deinococcus radiodurans suggests that the presence of the archaeal-type ATPase is a primitive character of the Deinococci that was acquired through horizontal gene transfer (HGT). However, the presence of a bacterial type F-ATPases was reported in two newly identified Thermus species (Thermus scotoductus DSM 8553 and Thermus filiformis DSM 4687). Two different scenarios can explain this finding, either the recent replacement of the ancestral A/V-type ATPase in Thermus scotoductus and Thermus filiformis with a newly acquired F-type ATPase or a long-term persistence of both F and A type ATPase in the Deinococci, which would imply several independent losses of the F-type ATPase in the Deinococci. Using PCR with redundant primers, sequencing and Southern blot analyses, we tried to confirm the presence of an F-type ATPase in the genome of Thermus scotoductus and Thermus filiformis, and determine its phylogenetic affinities. Initial experiments appeared to confirm the presence of an F-type ATPase in Thermus scotoductus that was similar to the F-ATPases found in Bacillus. However, further experiments revealed that the detection of an F-ATPase was due to a culture contamination. For all the Thermus and Deinococcus species surveyed, including Thermus scotoductus, cultures that were free of contamination only contained an A/V-type ATP synthases.