Nitratifractor salsuginis Nakagawa et al. 2005 is the type species of the genus Nitratifractor, a member of the family Nautiliaceae. The species is of interest because of its high capacity for nitrate reduction via conversion to N(2) through respiration, which is a key compound in plant nutrition. The strain is also of interest because it represents the first mesophilic and facultatively anaerobic member of the Epsilonproteobacteria reported to grow on molecular hydrogen. This is the first completed genome sequence of a member of the genus Nitratifractor and the second sequence from the family Nautiliaceae. The 2,101,285 bp long genome with its 2,121 protein-coding and 54 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.