Integrated bioremediation systems are widely emerging treatment of mariculture wastewaters. The system consists of several units including the biofilm which is microbial consortium that help in removal of waste nutrients. However, a great performance would have been achieved if there was an addition of exogenous compound bacteria (ECB) in the biofilm unit. In this study, the ECB were added to the biofilm unit of an artificially created integrated mariculture wastewater system to explore their influence on the microbial community composition and structural diversity. A high-throughput amplicon of 16 S rRNA, PERMANOVA and LDA Effect Size (LEfSe) analyses were used to investigate the effects of ECB on the microbial community and nutrients removal performance in the biofilm unit of the integrated bioremediation systems of aquaculture wastewater (ISBAW). The results showed that the contents of total phosphorus (TP), chemical oxygen demand (CODMn), ammonia nitrogen (NH4+-N), and nitrate (NO3--N) decreased significantly after the treatment of ECB with the removal rates of 68%, 58%, 75% and 84%, respectively. The bacterial community in the water column has experienced three successional stages: the pretreatment, the middle and the late stage. The biofilm has gone through two successional stages: the pretreatment - early stage and the late stage. Bacillus became potential biomarker in the late water column and the pretreatment biofilm, respectively. Random processes were closed correlated with the community in the water column while deterministic processes were closely correlated to the biofilm’s component. Generally, the addition of ECB significantly affects the structural composition of bacterial communities on different media in the biofilm unit. The study provides basic information for understanding and development of efficient and optimized the IBSAW.