Until now, ten anammox species have been described, including seven that are available in laboratory enrichment cultures. All have the taxonomical status of Candidatus, as none were obtained as classical pure cultures. Known species are divided over five genera: 
# Kuenenia, one species: Kuenenia stuttgartiensis. 
# Brocadia, three species: B. anammoxidans, B. fulgida, and B. sinica. 
# Anammoxoglobus, one species: A. propionicus. 
# Jettenia, one species: J. asiatica. 
# Scalindua, four species: S. brodae, S. sorokinii, S. wagneri, and S. profunda. 
Representatives of the first four genera were enriched from sludge from wastewater treatment plants; K. stuttgartiensis, B. anammoxidans, B. fulgida, and A. propionicus were even obtained from the same inoculum. Scalindua dominates the marine environment, but is also found in some freshwater ecosystems and wastewater treatment plants. 
Together, these 10 species likely only represent a minute fraction of anammox biodiversity. For instance, there are currently over 2000 16S rRNA gene sequences affiliated with anammox bacteria that have been deposited to the Genbank (https://www.ncbi.nlm.nih.gov/genbank/), representing an overlooked continuum of species, subspecies, and strains, each apparently having found its specific niche in the wide variety of habitats where anammox bacteria are encountered. Species microdiversity is particularly impressive for the marine representative Scalindua. A question that remains to be investigated is which environmental factors determine species differentiation among anammox bacteria.
The sequence identities of the anammox 16S rRNA genes range from 87 to 99%, and phylogenetic analysis places them all within the phylum Planctomycetota, which form the PVC superphylum together with Verrucomicrobia and Chlamydiae. Within the Planctomycetota, anammox bacteria deeply branch as a monophyletic clade. Their phylogenetic position together with a broad range of specific physiological, cellular, and molecular traits give anammox bacteria their own order Brocadiales.