Abstract: Backgorund: The activities of NH4+ and NO2– oxidizing bacteria in aquaculture recirculating system can influence to environmental N-inorganic, physiologic response and growth performance of mud crab Scylla serrata. The culture of mud crab in a Recirculating Aquaculture System (RAS) involves the microbiological nitrogen removal including aerobic and anaerobic nitrogen conversion such as nitrification and denitrification. In nitrification process activities of ammonium (NH4+) and nitrite (NO2–) oxidizing bacteria can influence for a Dissolved Inorganic Nitrogen (DIN) like as ammonia (NH3–), nitrite (NO2–) and nitrate (NO3–) in the RAS environmental. Objective: The objective of this study aimed to isolate and determine the activities of ammonium (NH4+) and nitrite (NO2–) oxidizing bacteria in crab culture using a recirculating aquaculture system. Materials and Methods: With different quantities of shelters (4 and 6 shelters) in box cultivation of mud crab, the activity oxidizing bacteria be count by amount of NH4+, NO2– and NO3–. The concentrations of ammonia, nitrite and nitrate be measured with spectrophotometers in the Environmental and Microbiology Laboratory, Bogor Agricultural University. Ammonium (NH4+) and nitrite (NO2–) oxidizing activity tests were used to determine the enzyme activity and affinity to the culture substrate. Results: Based on the Michaelis-Menten kinetics analysis for ammonia oxidizer, it was found that treatment P4 showed a Vmax value (Maximum speed) of 0.073 mM h–1 and a Km (Michaelis-Menten) constant was 0.1909 mM. Whereas treatment P6 showed lower values, i.e., Vmax of 0.0673 mM h–1 and Km of 0.0788 mM, indicating that the affinity of enzymes related to ammonium oxidation by the bacteria in this treatment was higher. Conclusion: This study showed P6 give the best of NH4+ oxidizer activity and this was supported by the higher ammonium oxidation rate (12.72±5.89 μM h–1).