To reduce fresh water load on ships, seawater can be used for toilet flushing on-board. And saline black water was treated on-site by bioaugmentation original marine bacteria with Pseudoalteromonas sp. SCSE709-6 (P. sp. SCSE709-6) to prevent marine pollution. In the batch experiments, P. sp. SCSE709-6 was effective in nutrient removal, which was not closely related to the amount of inoculation. In the on-board continuous experiments, the systems inoculated with P. sp. SCSE709-6 possessed excellent TP removal ability (removal rate: 80.93% for T3 and 88.39% for T4). The inoculum of P. sp. SCSE709-6 changed the microbial community structure and increased the similarity of microbial communities. P. sp. SCSE709-6 had a significant influence on the performance and microbial community of the systems. This study strongly proposes that the P. sp. SCSE709-6 is a promising alternative in saline black water treatment, which has great significance to the practice of on-board seawater flushing toilet.