We compiled and analyzed long-term time-series data collected in Korea to evaluate changes in oceanographic conditions and marine ecosystems near Jeju Island ($33^{circ}00^{prime}-34^{circ}00^{prime};N$, $125^{circ}30^{prime}-127^{circ}30^{prime};E$) from 1981 to 2010. Environmental data included depth-specific time series of temperature and salinity that have been measured bimonthly since 1961 in water columns at 175 fixed stations along 22 oceanographic lines in Korean waters by the National Fisheries Research & Development Institute, and time series of estimated volume transport of the Tsushima Warm Current (TWC) and Korea Strait Bottom Cold Water (KSBCW) for the period from 1961 to 2008. We analyzed the species composition in terms of biomass of fish species caught by Korean fishing vessels in the waters near Jeju Island (1981-2010). Data were summarized and related to environmental changes using canonical correspondence analysis (CCA). The CCA detected major shifts in fish community structure between 1982 and 1983 and between 1990 and 1992; the dominant species were a filefish during 1981-1992 and chub mackerel from 1992 to 2007. CCA suggested that water temperature and salinity in the mixed layer and the volume transport of the TWC and the KSBCW were significantly related to the long-term changes in the fish community in the waters off Jeju Island. Fish community shifts seemed to be related to the well-established 1989 regime shift in the North Pacific. Further studies are required to elucidate the mechanisms driving climate change effects on the thermal windows and habitat ranges of commercial species to develop fisheries management plans based on reliable projections of long-term changes in the oceanographic conditions in waters off Jeju Island.