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 high abundance and biomass of Benthosema pterotum is one of the keystone species in the coastal water at Fanshan, Pintung County. 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. The high landings of Benthosema pterotum indirectly reduce the abundance of demersal fish from ecosystem, and the abundance of epipelagic species is increasing. This trend of fish abundance matched the time series trends of fish abundance in the landing of bottom trawl surveys at Fanshan, Pintung County. From 2008, the richness, abundance, biomass, diversity indices, and multivariate analyses of fish community did not show any statistically significant trend over year. However the fisheries stress is persist in high level, the L50 is still low. Mesh regulation may be the resolution for sustainable fisheries.