There are two treatment processes that are currently applied to ships are the biological treatment process using the activated sludge and the electrochemical treatment. However, neither of them are able to remove both nitrogen and phosphorus due to their limited ability to remove organic matters, which are main causes of the red tide. This study was conducted to identify the characteristics of nitrogen removal factors from manure wastewater by replacing the final settling tank in SBR (Sequencing Batch Reactor) process and applying immersion type hollow fiber membrane. SBR process is known to have an advantage of the least land requirement in special environment such as in ship and the immersion type hollow fiber membrane is more stable in water quality change. As the result, the average in the cases of DO (Dissolved Oxygen) is 2.9(0. 6∼3.9) mg/L which was determined to be the denitrifying microorganism activity in anaerobic conditions. The average in the cases of ORP (Oxidation Reduction Potential) is 98.4∼237.3 mV which was determined to be the termination of nitrification since the inflection point was formed on the ORP curve due to decrease in the stirring treatment after the aeration, same as in the cases of DO. Little or no variation in the pH was determined to have positive effect on the nitrification. T-N (Total Nitrigen) removal efficiencies of the finally treated water were 71.4%, 72.3% and 66.5% in relatively average figures, thus was not a distinct prominence. In being applied in ships in the future, the operating conditions and structure improvements are deemed necessary since the MEPC (Marine Environment Protection Committee). 227(64) ship sewage nitrogen is less than the standard of 20 Qi/Qe mg/L or the removal rate of 70%.