Anaerobic ammonium-oxidizing (anammox) bacterium, Candidatus Brocadia sp. 40 demonstrated the fastest growth rate compared to others in this taxon. A draft genome sequence of the bacterium was determined. A 2.93-Mb genome sequence was assembled, in which 3,109 gene-coding regions, 43 tRNAs, and a single rrn operon were annotated.