A method is provided for detecting the presence or absence of salmonid pathogens, including Infectious Hematopoietic Necrosis Virus (IHNV), Infectious Pancreatic Virus (IPNV), Infectious Salmon Anemia Virus (ISAV), Salmon Alphaviruses (SAV), Viral Hemorrhagic Septicemia Virus (VHSV), and Renibacterium salmoninarum. The method includes steps which may be carried out using a variety of analytical techniques, such as multiplexing RT-PCR, Target Specific Primer Extension (TSPE), and fluidic bead-based technology. PCR primers and TSPE primers which are components of the multiplex diagnostic assay using fluidic bead-based technology for detection of salmonid pathogens are also described.