Seasonal changes of zooplankton communities were monitored at two coastal marine areas, Uchiumi and Fukuura Bays located at the Uwa Sea, east side of Bungo Channel. The two sites are close to each other (c.a. 20 km) with similar habitat environments, but receive different environmental stresses from aquaculture activities, pearl oyster farming for Uchiumi Bay and fish farming for Fukuura Bay. Since both bays have no inflowing river and small populations in the catchment, the impacts of different aquaculture activities on meso- and microzooplankton communities were compared. As results, Fukuura Bay showed higher ammonium and phosphate concentrations, suggesting that fish farming could accelerate eutrophication more seriously. The dominant species of mesozooplankton were similar at the two sampling sites with dominance of small coastal calanoid copepod, Paracalanus spp., but the abundances of larger calanoid species, Calanidae, Eucalanidae, Temoridae and Acartiidae, were markedly higher in Uchiumi Bay. Small cyclopoid copepods, Oithona spp. were abundant at both sites, but the densities varied seasonally, and often more abundant at Fukuura Bay. The abundances of microzooplankton including rotifers and small Oithona copepodids were higher at Fukuura Bay. Results suggest that fish farms accompanying discharge of nutrients from additional food supply for fish may seriously modify zooplankton community structure by decreasing the abundance of mesozooplankton through accelerating the eutrophication of coastal waters.