Three methods for identifying Enterococcus spp. and E. faecalis were compared. Using conventional culture methods, 99 isolates from rainbow trout (Oncorhynchus mykiss Walbaum) and water samples were identified as Enterococcus spp. and 86.7% of these were identified as E. faecalis. Using the oligonucleotide probes Eub338, NonEub, Enc145, Efs129, and Str, fluorescence in situ hybridization (FISH) identified 73.7% of the 99 Enterococcus spp. as Enterococcus spp. and 58.6% as E. faecalis. Using polymerase chain reaction (PCR) methods, 88.9% of the 99 samples were identified as Enterococcus spp., 36.4% as E. faecalis, and none as E. faecium. Thus, the consistency between conventional, FISH, and PCR methods was inadequate.