Insects of the genus Wiseana (Lepidoptera: Hepialidae) are major agricultural pests in New Zealand. Singly enveloped nucleopolyhedroviruses (SNPVs) isolated from three of the seven described Wiseana species have potential as biological control agents. As part of an effort to characterise the Wiseana SNPV genome the polyhedrin gene was cloned and the nucleotide sequence determined. The gene sequence was used, in conjunction with morphological and restriction endonuclease analysis, to compare isolates from different sites and species of Wiseana. Heterogeneity was detected within a single site, as well as between SNPV from separate Wiseana species. The extent of divergence between the nucleotide sequences was small enough, however, to consider three SNPVs from W. signata, W. cervinata and W. umbraculata as different strains of a single SNPV species. This improves the likely practicability of developing a single viral agent to control this pest complex. In addition, the virus polyhedrin gene sequence was used to estimate the phylogenetic relatedness of a W. signata SNPV to 16 other NPV from diverse insect genera. These comparisons suggest the Wiseana SNPV was unique within the Baculoviridae, but was more closely related to the group II NPVs.