An activated sludge process with partial nitrification (AS/PN) in combination with anaerobic ammonium oxidation (Anammox) process for treatment of seafood processing wastewater was developed and investigated in this research. Operating conditions of AS/PN process for coupling with Anammox process were identified as pH between 7.7–8.2 and DO as 0.5–0.9 mg L−1 to achieve over 85% COD removal as well as partial nitrification. The developed AS/PN process could produce almost equal concentration of ammonium and nitrite nitrogen in the effluent which was highly suitable for the Anammox process. Near complete removal of ammonium and nitrite was achieved during steady state Anammox process operation. Maximum nitrogen removal rate for the Anammox process was found to be 0.6 kg N m− 3 d−1. Microorganisms involved in both AS/PN and Anammox processes were identified using in situ hybridization and polymerase chain reaction techniques. The result 16S rDNA revealed 94% homology to Candidatus “Brocadia fulgida.”