Seasonal variation in the biomass of eelgrass (Zostera marina) and epiphytic algae in two eelgrass beds (Dongdae and Aenggang Bay) around Namhae Island was investigated throughout 2005. Shoot density and eelgrass biomass differed across months and locations. Peak shoot density occurred from April to August 2005, whereas eelgrass biomass was higher in July and August 2005. Shoot density as well as eelgrass biomass were higher in Dongdae Bay compared to Aenggang Bay. A total of 21 epiphytic algal species (4 Chlorophyta, 2 Phaeophyta, and 15 Rhodophyta) were collected, and dominant species included Polysiphonia japonica, Lomentaria hakodantensis, Symphyocladia latiuscula, Champia sp., and Heterosiphonia japonica. Seasonal variation in both the species composition and biomass of epiphytic algae was substantial: peak epiphytic algal biomass occurred in January and December 2005. We also observed high epiphytic algal biomass in the eelgrass bed of Dongdae Bay. Seasonal changes in the biomass of eelgrass and epiphytic algae were primarily influenced by water temperature, whereas those of the epiphytic algal community were also correlated with eelgrass (substrate) morphology and growth, the life cycle of epiphytic algae, and physical characteristics within eelgrass beds. The spatial variation of eelgrass density and biomass were also limited by sediment characteristics.