In the present study, autotrophic ammonia oxidizing bacteria (AOB) were isolated and characterized from a fish processing effluent treatment plant. Sequencing of 16S rRNA gene showed AOB affiliation to Nitrosomonas marina, Nitrosomonas nitrosa and Nitrosospira lineages of Betaproteobacteria. The isolates were further confirmed with using ammonia mono-oxygenase subunit-A gene (amoA) specific fluorescence in situ hybridization assay. The reduction of ammonia by these isolates was comparable with the standard AOB pure culture Nitrosomonas europaea ATCC 19718. Among all the cultures, AOB-21 was found to be having highest potential for ammonia removal. The presence of AOB in fish processing effluent treatment plants suggests the usefulness of these isolates in sustainable removal of ammonia from fish processing waste effluent.