Anammox bacteria can perform anaerobic ammonium oxidation, a long missing process which contributes 30%~50% to dinitrogen gas in marine nitrogen cycling. The potential role of anammox bacteria coupling with ammonium oxidizing bacteria and archaea will benefit to elaborate the complex mechanism of marine nitrogen cycling. Furthermore, the unique cell and genomic characteristics make anammox bacteria an important model microorganism to explore the bacterial evolution. Here we re-viewed the current status of molecular ecology of marine anammox bacteria and give a perspective into the future based on our understanding of the literature and our own work.