Diagnostic monitoring in fish farms with land-based tanks and net cases was conducted in eastern, western, southern and Jeju island of Korea for the summer period from 2000 to 2006. Total 3,518-fish samples of marine and freshwater fishes in 25 fish species were tested for pathogens. Fish species tested were olive flounder (Paralichthys olivaceus), fleshy prawn (Fenneropenaeus chinensis Osbeck), black rockfish (Sebastes schlegeli), rock bream (Oplegnathus fasciatus), red sea bream (Pagrus major), black seabream (Acanthopagrus schlegeli), sea bass (Lateolabrax japinicus), gray mullet (Mugil cephalus), rainbow trout (Onchorhynchus mykiss) and others. The infection rates by bacterial pathogens in the years of 2000, 2001, 2002, 2003, 2004, 2005 and 2006 were 22.4%, 34.5%, 14.1%, 15.3%, 17.7%, 13.5% and 5%, respectively. The infection rates by parasitic pathogens were 20%, 33.8%, 12.4%, 14.1%, 9.2%, 10.5% and 10.7%, respectively. The infection rates by viral pathogens were 22.4%, 13.5%, 10.3%, 5.4%, 9.7%, 10.2% and 15.8%, respectively. The infection rates by mixed pathogens were 10.3%, 0%, 44.9%, 50.9%, 31.9%, 38.4% and 39.6%, respectively. The rates of mixed infections were very low until 2001. The rates were higher than those of singer infections from 2002 to 2006. During the diagnostic monitoring from 2000 to 2006, the main bacterial pathogens were Vibrio (41.2%) and Streptococcus (28.8%). The infection rate by protozoa (85.7%) mainly including Scuticociliates and Trichodina was highest. The infection rate by viral necrosis virus (VNNV, 42.2%) was the highest of the viral pathogens.