Fish community structure between eelgrass beds and an adjacent unvegetated area was investigated. Fishes were collected monthly from two eelgrass beds (Gamak and Yeoja Bays) and one adjacent unvegetated area in the southern sea of Korea between February 2006 and February 2007. The number of species for the Gamak and Yeoja Bays were 33, 28, respectively, while 28 species were identified from the unvegetated area. Leiognathus nuchalis was dominant in both Gamak and Yeoja Bays, while Engraulis japonicus was dominant in the unvegetated area. Cluster analysis conducted on total number of individuals for each species produced 3 groups; group A (appeared only in winter regardless of eelgrass), group B (appeared in eelgrass beds during all seasons except winter) and group C (appeared in the unvegetated area during all seasons except winter). The most important differentiating species between eelgrass beds and the unvegetated area were Lateolabrax japonicus, L. nuchalis, Takifugu niphobles and Pholis nebulosa. Based on the results of this study we can assume that eelgrass beds function as a nursery ground for young fishes from spring to fall, but not in winter.