The salinity effect on anammox bacteria has been widely reported; however, rare studies describe the microbial dynamics of anammox-based process response to the introduction of real seawater at mainstream conditions. In this study, an anammox process at mainstream conditions without pre-enriching anammox bacteria was shifted to the feeds of a synthetic wastewater with a portion of seawater mixture. It achieved over 0.180 kg-N/(m(3) day) of nitrogen removal rate with an additional seawater proportion of 20% in the influent. The bacterial biodiversity was significantly increased with the increase of seawater proportions. High relative abundance of anammox bacteria (34.24-39.92%) related to Ca. Brocadia was enriched and acclimated to the saline environment. However, the introduction of seawater caused the enrichment of nitrite-oxidizing Ca. Nitrospira, which was responsible for the deterioration of nitrogen removal efficiency. Possible adaptation metabolisms in anammox bacteria and other nitrogen transforming bacteria are discussed. These results highlight the importance of microbial diversity for anammox process under the saline environments of 20% and 40% seawater composition.