In this study, the community structure of marine benthic invertebrates was examined to evaluate the differences between the west, south, and east coasts of Korea and to identify the indicator species representing each region. Acrylic attachment plate sets were installed in Jeongok, Mokpo, Tongyeong, Yangpo, and Gangreung, and the invertebrate fauna thus captured were identified. Monitoring was performed in each area from March 2017 to May 2018. Water depth, temperature, and salinity at each location were measured to determine the potential influence of abiotic factors on the community structure. As a result, the mean depth of plates installed and the water temperature were significantly different in each area. A total of 32 invertebrate species were identified in all localities, and the most significant difference in the species compositions was found between Mokpo and Gangreung. The community structure differed significantly with a change in the plate depth, and a larger number of indicator species appeared on shallower plates. Finally, we determined the community structure of benthic invertebrates in different geographical regions of the Korean ocean by characterizing the dominant invertebrate taxa and the indicator species at each site.