Jeju Island in Korea has a suitable environment for land-based flounder culture with its coastal seawater temperature of 13–28?. Jeju Island’s cultured flounder has a production volume of 20,243 M/T and a production value of $157 million (2019), accounting for 54% of Korea’s cultured flounder production. However, with the expansion of the flounder culture industry and the long history of aquaculture, various diseases have been found in the species. Herein, we selected 20 flounder farms in Jeju Island, with independent environmental conditions, and examined parasites in cultured flounder once a month from January to December, 2019, for a total of 240 times. From the results, a total of 342 parasitic infection cases were identified; comprising 215 (62.9%) ectoparasitic and 127 (37.1%) endoparasitic infections. Seven ectoparasitic infections were identified, namely, Trichodina sp., 86; Scuticosiliate (Miamiensis avidus), 79; Ichthyobodo sp., 16; Gill protozoa, 16; Amoeba sp., 7; Cryptocaryon irritans,4; Gyrodactylus sp., 4; and Kudoa sp., 3 cases. Trichodina sp. comprised the highest number of infection cases but the damage on cultured flounder was relatively insignificant, and it did not cause much problem if the water circulation was smooth. Scuticosiliate comprised the second highest number of infection cases; it penetrates the skin, muscle, gill, and brain tissues in young flounders (< 200 g), causing necrosis, and eventually death. Other ectoparasites did not cause many infections or significant damage. Six species of endoparasites, which infect flounders’ internal organs, muscles, and bladders were identified, namely, Parvicapsular sp., 59; Enteromyxum leei, 34, Myxodavicia sp., 16; Sinuolinea sp., 10; Owrtholinea sp., 5; and Kudoa sp., 3 cases. Many cases of endoparasitic infections, mostly Myxosporea, were found recently. Besides the E. leei infection, the damage caused by these parasites is either mild or uncertain. However, when E. leei infects the intestines, it causes emaciation disease, which can result in secondary bacterial infection and death.