Between July 2004 and January 2005, high mortalities (up to 80-100%) were frequently encountered in postlarvae of Macrobrachium rosenbergii in southern Taiwan. Pathologically, eosinophilic intranuclear inclusion bodies (INIs) were found only in the hepatopancreatic tubular epithelial cells of the infected postlarvae from hatchery farms. No lesions could be detected in tissue of ectodermal or mesodermal origin. Interestingly, different lesions were found in sub-adults collected from a grow-out farm. Atrophic changes in abdominal muscles from the fourth to sixth segment and tail fan, associated with a reddish discoloration, were prominent features in these shrimp, but there was no unusual mortality or INI formation. In PCR assays for the detection of infectious hypodermal and haematopoietic necrosis virus (IHHNV), hepatopancreatic parvovirus (HPV), white spot syndrome virus (WSSV), Taura syndrome virus (TSV), yellowhead virus (YHV), M. rosenbergii nodavirus (MrNV) and extra small virus (XSV), only an expected 389-bp product, specific for the IHHNV nonstructural protein gene, was obtained from all postlarvae and sub-adults examined. Positive reactions to in situ hybridization, using a DIG-labelled DNA probe, further confirmed IHHNV as the causative agent. In a comparison of our strains with Taiwanese (GenBank accession no. AY 355306 and AY 355308) and American strains (GenBank accession no. AF218266 and AF273215), nucleotide sequence identities were up to 99.7%. This is the first report concerning natural infection of IHHNV in postlarvae and sub-adults of M. rosenbergii.