Aquaculture has expanded largely in recent decades, which has caused negative impacts on coastal marine ecosystem especially from the respect of organic and nutrient pollution. Among the aquaculture products, more than 25% is derived from farming non-indigenous species (NIS) . Culturing NIS has ecological risks since the most dramatic ecosystem changes have been found in areas after rapid growth of NIS. China is an aquaculture country. Argopecten irradians (Lamarck, 1819) culturing in open sea and Penaeus vannamei (Boone, 1931) culture in ponds are two of the most popular aquaculture NIS, which both have high loading (faeces or feeds) onto the bottom. Such loading might have a strong impact on benthic environment. Monitoring changes in benthic communities has proven to be a useful signal of impact from aquaculture. Meiofauna, due to their small size, high turnouver and lack of larval dispersion, is becoming the most popular tool in environmental monitoring. Moreover, the trophic relationships of benthos are not well learned under the aquaculture environment, especially it comes NIS farming issue. This is the first study designed to investigate the effects on meiobethos (in both community structure and trophic level) of NIS A. irradians (in the case of open water) and P. vannamei (in the case of pond) , aiming to quantifying the impact of NIS introduced by aquaculture on the ecosystem functioning. Environmental parameters are monitored at the same time.