Bottom trawl fishery is receiving more and more attentions these years because of its highly by-catch rate and serious damage to the seabed. Fishery management will need to protect the habitats and the environment to maintain biodiversity and resources sustainable. In Taiwan, studies in the past were usually focused on single specie or stock, very few papers studied fisheries from community and ecosystem approach. We don’t have many data on the species composition and the by-catch information. Therefore, the purpose of the present study is to study the community structure of bottom trawl fishes from the two traditional trawl fishery grounds in Aoti and Tahsi, north-eastern Taiwan and one non-traditional fishing ground, Cinshan in northern Taiwan.