Hepatopancreatic parvovirus infection is associated with reduced growth rates of prawns during the juvenile stages and overt mortalities. Hepatopancreatic parvovirus was purified from Penaeus merguiensis from northern Queensland and a partial consensus sequence of 5.9 kb was obtained. Nucleotide comparisons revealed that the Australian isolate of HPV has a nucleotide similarity (87%) closer to HPVchin and the full sequence of HPV Penaeus monodon (PmDNV) (6321 bp) than to HPVsemi (83%). Three putative open reading frames were identified. The first open reading frame encoded a nonstructural protein (NS2) and shared an amino acid similarity of 86% with PmDNV. The second ORF overlapped the first open reading frame and shared 93% and 26% amino acid similarity with PmDNV and PstDNV, respectively, and encoded NS1. The third ORF encoded the viral structural protein and shared an amino acid similarity of 73% with the capsid protein of PmDNV and HPVchin. The phylogeny suggests that the Australian HPV isolate is closely related to the Korean HPVchin isolate than to the Indian HPVsemi and Thai PmDNV isolates. HPV strains may be following the phylogenetic relationship of penaeid prawn hosts rather than their geography.