The western barred bandicoot (Perameles bougainville) is an endangered Australian marsupial species in which a papillomatosis and carcinomatosis syndrome occurs. Bandicoot papillomatosis carcinomatosis virus type 1 (BPCV1) is associated with the lesions of this progressively debilitating syndrome. Five digoxigenin-labelled DNA probes were generated for in situ hybridization (ISH) and the technique was optimized and performed on formalin-fixed paraffin-embedded (FFPE) biopsies. Staining of keratinoicyte and sebocyte, nuclei within lesions was achieved with all five probes. The sensitivity of ISH (76.9 %) surpassed that of PCR (30.8%) for FFPE samples. The sensitivity of ISH varied from 81 % (papillomas) and 70% (carcinoma in situ) to 29% (squamous cell carcinomas). The specificity of the test was confirmed using an irrelevant probe and papillomas from other species. These results strengthen the association between BPCV1 and the western barred bandicoot papillomatosis and carcinomatosis syndrome and give insight into the biology of the virus-host interaction.