To survey the seagrass distribution in Jeju and Chuja Islands, we directly observed seagrass beds using SCUBA in July, 2011. Distributional area, species composition, morphology, density, and biomass of seagrasses and environmental characteristics were examined in investigation sites. In particular, three protected seagrass species (Zostera marina, Z. caulescens and Z. caespitosa) were found in the investigation areas. While the three species were found in Chuja Island, only Z. marina was distributed in Jeju Island. Z. marina was distributed only north-eastern coast of Jeju Island, and the total coverage was 238,572m2. Total seagrass coverage of Chuja Island was 23,584m2. In detail, Z. caulescens Z. caespitosa and Z. marina were 21,216, 1,870 and 498m2, respectively. Of these, Z. marina was found from the intertidal to subtidal zones of 5m MSL (mean sea level) depth. Z. caespitosa and Z. caulescens were found in subtidal zones of 3~~4 m and 4~~6m MSL depth, respectively.