The antimicrobial resistance of 160 strains of Enterococcus faecalis and 173 strains of E. faecium to 12 antimicrobial agents was investigated. The test strains were isolated from 126 wild seawater and farmed fish, including olive flounder (Paralichthys olivaceus), black rock fish (Sebastes schlegeli), red sea bream (Pagrus major), and sea bass (Lateolabrax japonicus), in 2005 and 2006. Overall, 91.9% of the E. faecalis isolates and 88.4% of the E. faecium isolates showed antimicrobial resistance to at least one antimicrobial agent. The pattern of antimicrobial resistance of the isolates differed little according to the species of fish. The percentage of E. faecalis and E. faecium with specific antimicrobial resistance differed according to the sample source. For the isolates from farmed fish samples, 66.7% of E. faecalis were tetracycline resistant and 54.5% of E. faecium were erythromycin resistant. By contrast, in the wild fish seawater samples, 92.0% of E. faecalis were rifampin resistant and 88.5% of E. faecium were tetracycline resistant.