The method of cluster analysis was applied to analyze the seasonal differences of benthic community structure in the northern waters of Taiwan based on data collected from R/V Hai Fu, Fisheries Research Institute by bottom trawling from 2008 to 2009. During the survey period, a total of 216 fish species, belonging to 162 genera, 100 families, and 35 orders, were collected. According to the abundance rankings, just 14 species accounted for 86.21% of the total abundance of all fish. The average body weights of 145 species that accounted for 96.11% of the abundance and 56.53% of the biomass were lower than 50 g. In addition, the mean body weights of 27 species were between 51-l00 g, and the mean body weights of 44 species were over 101 g. The dominant species included skinnycheek lanternfish (Benthosema pterotum), glowbelly (Acropoma japonicum), red-spot prawn (Metapenaeopsis barbata), sixfinger threadfin (Polydactylus sextarius), mitre squid (Uroteuthis chinensis), and bensasi goatfish (Upeneus japonicus). Cluster analysis showed seasonal communities can be divided into spring-summer and autumn-winter groups. Seasonal richness peaked in the autumn, but the highest evenness and diversity were in the winter. Results of the ABC method showed that the curves of abundance were all above the curves of biomass in each season, which indicated that the present benthic community structure in the northern waters of Taiwan was influenced by the overcapacity of the bottom trawl fishery.