In order to evaluate the feasibility and validity of using bagasse as the substrates in biological aerated filter (BAF), biofilms were cultured in BAF, based on which wastewater treatment system for marine aquaculture was established. The decomposing effect of BAF using bagasse as substrates was evaluated by monitoring the concentrations of water quality parameters such as total ammonia nitrogen (TAN), nitrite nitrogen (NO2--N), etc.. The result showed that it took 26 d for the BAF using bagasse as substrates to form biofilm, while the density of total heterotrophic bacteria and the bacillus attached in bagasse were 3×108 cfu/g and 7.8×107 cfu/g respectively. During the wastewater treatment, the concentrations of ammonia nitrogen and nitrite nitrogen were controlled below 0.2 mg/L and 0.05 mg/L respectively, and the density of bacillus increased from 3.3×103 cfu/L to 7×104 cfu/L, while that of vibrio decreased from 4.9×103 cfu/L to 3.1×101 cfu/L. The study indicates that bagasse as is very efficient in biomass formation, and is a preferable material for BAF in mariculture wastewater treatment.