To understand responses of marine ecosystems to climate changes in the northwestern Pacific, especially responses to the 1998 regime shift, we related month-specific variability in hydrographic conditions to long-term changes in mesozooplankton in four regions adjacent to the Korean peninsula: the eastern Yellow Sea (EYS), northern East China Sea (NECS), and southwestern and northwestern Japan/East Sea (SJES and NJES). Sea surface (10-m depth) temperature in February has increased since the early 1990s in all four regions. Sea surface temperature in April and June has increased since the late 1990s in the SJES and EYS. Surface salinity has decreased, especially since the late 1990s, except NJES. Biomass of mesozooplankton in Korean sea regions (the EYS, NECS and SJES) began to increase after the early 1990s, with sharp increases after the late 1990s, indicating a regime shift triggered by the increased seawater temperatures. Unusually higher biomass was also occasionally observed in April, June or October after the late 1990s in the EYS and NECS. Abundances of the four major zooplankton groups (copepods, amphipods, chaetognaths and euphausiids) have generally increased since the late 1990s. The pattern of change in zooplankton abundance varied depending on taxonomic group and region, but we concluded that the four seas responded to the 1989 or 1998 regime shifts with respect to water temperature, salinity and zooplankton. We detected an additional sudden shift in both the zooplankton community and fisheries catch in the Korean waters, which we speculated was associated with the strong 1982/1983 El Niño event. The 1982–1983 shift was characterized by increased dominance of copepods, and was pronounced in the EYS, which is strongly influenced by river discharge. The results highlight the need for further retrospective analyses of regional ecosystems.