During the 1990s many studies on zooplankton in the Japan Sea have been carried out. In this review, I have synthesized the study of horizontal distribution, seasonal and annual variations of zooplankton biomass, and ecological characteristics of major component species in the southern Japan Sea, which area is influenced by the warm Tsushima Current. The zooplankton biomass (annual mean) in the southern Japan Sea was lower than in the subarctic Pacific, including the northern Japan Sea, and similar to biomass levels in Kuroshio waters. Temporal variations in zooplankton biomass showed both seasonal and year-to-year components. Seasonal biomass increases to a maximum in spring with a weak secondary peak in autumn. As for long-term changes, 3–6 year cycles were identified, with the dynamics of the surface warm Tsushima Current and the subsurface cold water playing important roles in determining the yearly zooplankton community structure and biomass. Cold water species in the southern Japan Sea had extensive diel vertical migrations whose range is restricted in summer by the development of a thermocline. Among these species, the herbivores Euphausia pacifica and Metridia pacifica encounter a lower food supply, resulting in lower growth rates. The vertical dispersal of epipelagic carnivorous zooplankton such as Sagitta elegans and Themisto japonica to the deep-sea is probably facilitated by reduced interspecific competition. Their interaction with Japan Sea Proper Water, characterized by near-zero temperatures in the meso- and bathypelagic zones suppresses growth rates of the mesopelagic zooplankton. The lack of micronektonic predators in the mesopelagic zone may allow the persistence of slow growing populations.