Fish assemblages associated with eelgrass beds and unvegetated area were compared based on specimens collected every month in Jindong Bay. The common fish species were Hexagrammos otakii, Acanthopagrus schlegeli, Lateolabrax japonicus, Pholis nebulosa, P. fangi, Leiognathus nuchalis, Repomucenus valenciennei, and Acanthogobius flavimanus. H. otakii, A. schlegeli, P. nebulosa and L. japonicus were higher abundance in an eelgrass bed than unvegetated area, whereas P. fangi, R. valenciennei and A. flavimanus were higher in unvegetated area. Sillago japonica, Hippocampus japonica, Takifugu niphobles, Pseudoblennius percoides, Sebastes inermis, Syngnathus schlegeli, Sebastes schlegeli were found in an eelgrass bed, but not in unvegetated area. Most of fish species were primarily small fish species or juveniles of fish species in an eelgrass bed, while larger fish species were found in unvegetated area. The eelgrass bed in Jindong Bay seem to play a nursery role for fishes. Seasonal variations in both species composition and abundance were large in two habitats; higher number of species and individuals occurred May 2002, and April 2002 to July 2002, while biomass was the highest in April 2002 and July 2002. Fish numbers as well as biomass were lowest in January 2002. Species richness, number of individuals and biomass of fishes in an eelgrass bed were significantly higher than those of in unvegetated area. These result suggest that differences in fish species richness and abundances are primarily related to habitat structure. Different habitat preferences were evidenced for the juveniles and adult of several fish species.