Fish assemblages associated with rock reef and non-rock reef were studied using specimens collected at three sites in Geomun Island waters of the Southern Sea, Korea, in February, May, August and October, 2006. Two survey methods for the study were followed: collection by a gill net, and video observation by scuba diving. The gill-net survey was conducted during the night, the scuba-diving observations were conducted during the day. From the gill-net survey, a total of 40 species, 380 inds. and 71,426.9 g was caught at the three sites. The dominant species was Trachurus japonicus; other species were Raja kenojei, Dasyatis akajei, Stephanolepis cirrhifer, Narke japonica, Pagrus major, Sebastes inermis, and Sphyraena pinguis. At the rock-reef site, a total of 26 species, 264 inds. and 46,776.7 g was caught by gill net, and the dominant species was T. japonicus. A total of 17 species, 45 inds., 10,535.1 g was caught at the flat-bottom 1 site, and 19 species, 71 inds. and 14,115.1 g were caught at the flat-bottom 2 site. The scuba-diving survey resulted in 13 species and 1,749 inds. observed at the three sites through the survey period. The main observed fishes were rock-dwelling species such as Chromis notatus, Microcanthus strigatus, S. cirrhifer, Ditrema temmincki, Evistias acutriostris, Girella punctata, Halichoeres poecilopterus, Hexagrammos agrammus, Prionurus scalprum, Sebastes inermis, and Semicossyphus reticulatus. Seven species and 1,739 inds. observed at the rock-reef site comprised 99.4% of the inds. of the three sites. Therefore, the fish community in Geomun Island waters included many rock-reef. species, but a few were migratory species like T. japonicus and Scomber japonicus. The abundance of fish at the rock-reef site was high in comparison with those at two non-rock reefs. The dominant species were very different between the day and the night, although rock-reef species comprised the main part of the fish community. We conclude that the high abundance of fish in Geomun Island waters is most closely related to physical structure, such as rock reefs, which is the main habitat of many fishes.