Thirteen isolates of infectious pancreatic necrosis virus (IPNV) from eel and rainbow trout in Taiwan were compared with the selected serotypes AB, SP and VR-299 by PAGE analysis of their RNA genomes and early polypeptides. All the IPNV isolates from eels (1984 to 1986) from Lu Kang and Ping Tung, and from rainbow trout eggs and fry from Dan Sway (1985 to 1986) were most closely related to the AB serotype. However four rainbow trout isolates from Dan Sway (1984) had a similar RNA pattern to that of VR-299, whereas their early polypeptides were different, showing evidence of some mutations. Both RNA and polypeptide PAGE patterns were used to distinguish the isolates from known selected IPNV strains showing that this approach can be used for epizootiological studies.