Comparison of the species composition of benthos in the 10 and 100 m depths of coastal waters between Fanshan, Pintung County and Zihguan, Kaohsiung City revealed that Fish occupies the 98.6 % and 79.9 % of abundance and biomass respectively in the landings of artisanal bottom trawler at Fanshan, Pintung County which are higher than the fish abundance and biomass of benthos community in the other coastal waters around Taiwan. High abundance and biomass of Benthosema pterotum in the coastal water at Fanshan, Pintung County revealed that this species is one of the keystone species in the coastal ecosystem. The low stable isotope ratios of carbon and nitrogen revealed that this species has lower food chain status in food web to be consumed by many predatory species.