The main cause of annual fluctuations in catch and species composition of fisheries is usually uncertain, but a prevailing view has been that fishing effects are more critical than environmental variability. Filefish is a good anecdote: many Korean fisheries scientists have attributed the sudden collapse of Korean filefish fisheries in the early 1990s to overfishing, especially by trawl fisheries in the northern East China Sea (NECS). However, interdisciplinary researches have revealed that climate-driven, multi-decadal variability in oceanic conditions impacts both fish and fisheries around the world. To test the two alternative hypotheses (i.e., fishing and climate) as the major cause of the sudden decline of filefish, we compared fisheries data of filefish from the adjacent countries of the NECS and analyzed oceanographic conditions in relation to changes in species composition of fish assemblages in the NECS. Results suggested that the basin-wide, 1989 regime shift in the North Pacific and the subsequent shrinkage of habitat range to the southwest were the major cause of the sudden decline of filefish catch in the NECS. Locally, shifts in water temperature and currents were identified in the NECS for the early 1990s, but further physiology-oriented researches are required to understand the detailed mechanism of climate-change effects on filefish stocks in the marginal seas of East Asia.