CandidatusBranchiomonas cysticola is recognized as the most prevalent bacterial agent causing epitheliocystis in Atlantic salmon (Salmo salar). Based on its partial 16S rRNA sequence, the bacterium has previously been found to be a member of Burkholderiales in the class Betaproteobacteria. Multilocus Sequence Analysis (MLSA) of the bacterium and 60 type strains of Betaproteobacteria using newly identified housekeeping genes (dnaK, rpoC,andfusA) and ribosomal subunit sequences (16S and 23S), instead supported the bacterium’s affiliation to Nitrosomodales. Taxonomic rank normalization by Relative Evolutionary Divergence (RED) showed the phylogenetic distinction betweenCand.B. cysticola and its closest related type strain to be at the family level. A novel bacterial family namedBranchiomonaceaehas thus been proposed to include a monophyletic clade of Betaproteobacteria exclusively associated with epitheliocystis in fish.Supplementary InformationThe online version contains supplementary material available at 10.1007/s00203-023-03581-1.