This study surveyed for the prevalence of parasites, bacteria and viruses in four fish species, olive flounder (Paralichthys olivaceus), red sea bream (Pagrus major), black sea bream (Acathopagrus schlegeli) and black rockfish (Sebastes schlegeli) in 2010. The survey was aimed to compare the pathogens detected from wild and cultured fish for an epidemiological study. Anisakis sp. was predominantly detected from wild olive flounder and red sea bream (58.6% and 41.7% respectively), but not from the cultured fishes, suggesting anisakid infection is rare in cultured fish. The wild fish get in contact with the anisakids through their prey such as small fishes or crustaceans which carry the anisakids; whereas the cultured fish are fed with formulated feed, free of anisakids. Bacterial detection rates from the wild fishes examined in the study were lower than those of cultured fishes. Vibrio sp. dominated among detected bacterial population in cultured olive flounder (18%). Since vibriosis is known as a secondary infection caused by other stressful factors such as parasitic infections, handling and chemical treatment, it seems that cultured olive flounder are exposed to stressful environment. Viruses diagnosed in the study showed difference in distribution between wild and cultured fishes; hirame rhabdovirus (HRV) (0.1%) and lymphocystis disease virus (LCDV) (3.9%) were detected in the cultured olive flounder, but not in the wild fish, and marine birnavirus (MBV) (1.7%) and red sea bream iridovirus (RSIV) (3.2%) were detected from the wild and cultured red sea bream, respectively. From the survey conducted, it can be concluded that even though some pathogens (Trichodina sp., Microcotyle sp., etc.) are detected from both the wild and cultured fish, pathogens such as Anisakis sp., Vibrio sp. and LCDV showed difference in distribution in the wild and cultured host of same fish species and this can be attributed to their environmental condition and feeding.