The seasonal variations in species composition of set net fisheries were investigated in the eastern coast of Korea, from 2007 to 2008. In total, 51 species were found that were classified into 15 orders and 33 families. The water temperature of the study area was 0.1–2.1 °C during the study period, which was higher than the average water temperature in the last decade. Monthly variation in the number of species peaked twice, in May (spring) and November (autumn) when the water temperature increased and decreased, respectively, and monthly variation in the number of individuals showed a remarkably high trend in winter and autumn and was mainly caused by large migratory species. Based on the cluster analysis of the 18 most dominant species with more than 0.4% of the total number of individuals, we divided the species composition and community structure into three groups: fishes with temporary appearance (Group A), fishes with long-term appearance (Group B), and dominant pelagic fishes appearing with long-term appearance (Group C). We could conclude that seasonal variation in the fish community structure was mainly caused by pelagic migration of species under high water temperature conditions during the study period.