A novel anaerobic ammonium-oxidizing (anammox) bacterium was detected in an upflow column reactor treating synthetic nitrogen-rich saline solution. Here, we assembled a 4.59-Mb draft genome sequence of this bacterium, identified as a member of the genus “
Candidatus
Scalindua,” that has 84% nucleotide-level genomic similarity with the closest related anammox bacterium (“
Candidatus
Scalindua rubra”).