In coastal areas of China, high-density aquaculture has caused environmental problems and fish health concerns. Bacillus subtilis D9 is a new strain isolated from coastal soils which could be used in aquaculture to improve the water environment. We investigated the effect of B. subtilis D9 on the purification of coastal aquaculture wastewater and the resistance of grass carp Ctenopharyngodon idellus to pathogenic Vibrio infection. Three inoculation levels of B. subtilis D9 were used (5.5 × 107, 5.5 × 108 and 5.5×109 cfu ml-1 as BD7, BD8 and BD9, respectively), together with sterilized saline water without B. subtilis D9 as the Control. B. subtilis D9 at the inoculation level of BD8 showed the best performance with 81, 87, 91, 52 and 86% removal of NH4+-N, NO3--N, total nitrogen (TN), NO2--N and turbidity, respectively, after 25 d of treatment. These values were significantly higher than at the BD7, BD9 and Control levels. Under aeration (AIR) conditions, B. subtilis D9 at the inoculation level of BD8 showed removal efficiency of 93, 91, 95, 76 and 89%, respectively. In contrast it was only 26, 29, 16, 10 and 57% in an inactivated bacteria liquid (IBL) treatment. After 22 d of infection by Vibrio parahaemolyticus, significant differences were found in weight gain, specific growth rate and relative percentage of survival among grass carp grown on AIR, BD8 or IBL wastewater. In summary, B. subtilis D9 with aeration has beneficial effects on the purification of coastal aquaculture wastewater and on the resistance of grass carp to disease caused by V. parahaemolyticus.