Our aim was to compare the community structure of fish in the coast of Wando Island between 2001 and 2013. Using a gape net with wings, we collected 61 taxa, wherein the most dominant species was Engraulis japonicus. The sea temperature in the middle layer of the survey station in 2001 (after June) was obviously higher than that in 2013, which was < $20^{circ}C$. Except for Thryssa kammalensis in 2013, the log transformed individuals of seven dominant species, selected using a SIMPER (similarity-percentages procedure) analysis, decreased. Decreases in the individuals of Gobiidae spp., the warm-water species Trichiurus japonicus and Conger myriaster, and the migratory species Syngnathus schlegeli, Setipinna taty and Sardinella zunasi, which arrive in the southern coastal waters of Korea during summer-autumn, could be due to decreasing sea temperature in 2013. Thus, fish species diversity, estimated from rarefaction and k-dominance curves, declined in the coastal waters of Wando Island from 2001 to 2013, resulting in a significant difference in fish community structure.