A multiplex PCR assay based on the 16S rRNA genes was developed for the simultaneous detection of three major fish pathogens, Aeromonas salmonicida, Flavobacterium psychrophilum, and Yersinia ruckeri. The assay proved to be specific and as sensitive as each single PCR assay, with detection limits in the range of 6, 0.6, and 27 CFU for A. salmonicida, F. psychrophilum, and Y. ruckeri, respectively. The assay was useful for the detection of the bacteria in artificially infected fish as well as in fish farm outbreaks. Results revealed that this multiplex PCR system permits a specific, sensitive, reproducible, and rapid method for the routine laboratory diagnosis of infections produced by these three bacteria.Major pathogens involved in fish farm salmonid infections include the gram negative species Flavobacterium psychrophilum, Yersinia ruckeri, and Aeromonas salmonicida. They are the etiological agents of cold water disease, enteric red mouth disease, and furunculosis, respectively. These pathologies are common worldwide and produce considerable economic losses in the fish farming industry.Cold water disease particularly affects juvenile fish (3), and the causal agent is F. psychrophilum, a fastidious bacterium that is difficult to grow (12). The bacterium causes saddle-like external lesions near the dorsal fin and it can also be found in the mouth, spleen, and brain tissues. The fish may darken and develop bacteremia with the microorganism present throughout the animal. Y. ruckeri is an important pathogen in intensive aquaculture of trout and salmon. Disease outbreaks are related to stress (4), and little information is available about the biology of the bacterium. Infected fish present characteristic red eyes and mouth as well as internal hemorrhages. Diagnostic methods include culturing, serology, and molecular biology techniques (5, 9, 16). A. salmonicida also produces an infection in fish that causes muscle lesions which could produce ulcers on the surface of the skin and lead to septicemia. Different diagnostic methods have been developed, including enzymelinked immunosorbent assays (19,20), agglutination tests (11), and PCR probes (14).On the other hand, an efficient selective medium for reducing the growth of the background flora and facilitating the isolation and identification of each of these three bacteria species remains to be described. To combat these infections, vaccination has been shown to be an effective method for the prevention of enteric red mouth disease (17) and, less efficiently, for furunculosis (10, 13), but there is no effective control for cold water disease. In most cases, antimicrobial compounds should be used to control disease outbreaks caused by any of these microorganisms. Thus, a rapid and effective diagnostic method is essential for the application of specific treatment.Although multiplex PCR (m-PCR) has been widely applied to the detection of multiple viruses and bacteria in clinical specimens (2, 6, 7), it has not been applied to the detection of fish pathogens (1, 15). In th...