We examined seasonal succession in a phytoplankton and mesozooplankton community in open coastal waters with frequently occurring harmful algal blooms. Chlorophyll a (Chl a) concentration was positively related to the N/P/Si ratio, suggesting that nitrate is a major limiting nutrient for phytoplankton biomass increase. Heterotrophic red Noctiluca, but not toxic dinoflagellate, abundance showed a negative trend with both Chl a and mesozooplankton abundance. The phytoplankton community showed a clear seasonal succession, with an increased abundance of dinoflagellates in the summer community (June–September), which was distinctive from the autumn–winter–spring community (October–May) that was dominated by diatoms. A mesozooplankton community shift followed, with a lag of a couple of months, in the late August to December community that was associated with subtropical copepods. The other community from February to August is associated with marine cladocerans. Although the most dominant mesozooplankton of year was copepod at a rate of over 70%, coexisting gelatinous plankton such as appendicularians and Noctiluca, which may compete with copepods for prey could affect to copepod production in the region.