Recent advances in next generation sequencing has made it possible to sequence the entire virome of specific tissues, individuals, or whole organisms. To date, most virome sequencing or targeted virus sequencing has focused on viruses that are pathogenic to humans. However, exploration of the true extent of viral diversity in all species is central to understanding virus evolution and the origins of emerging viruses. In this study, we aimed to reveal the virome of various tissues in Australian wild rabbits (Oryctolagus cuniculus) together with associated fleas, to reveal whether viruses are shared between rabbits and invertebrates. Concurrently, we also examined the virome of several species of Australian calliphorid flies, commonly known as blowflies. These flies are frequently associated with transmission of pathogens in humans and animals, including rabbit haemorrhagic disease virus (RHDV). Tissue samples and fleas were collected from presumed healthy wild rabbits at two independent sites in the Australian Capital Territory (18 – 20 rabbits per site). Sampling of sympatric blowfly populations was conducted contemporaneously. RNA libraries were prepared from tissue-specific (liver, duodenum, caecal content, lung, whole blood, fleas or blowflies separated by species) and location-specific RNA pools for RNA sequencing on the Illumina HiSeq platform. The resulting sequencing reads were assembled and annotated to reveal a diverse array of characterised and uncharacterised viruses which were present in both invertebrates and rabbit tissues. Importantly, the bowflies, while carrying an extensive diversity of insect-specific viruses, also harboured a number of rabbit-specific viruses. For example, we discovered RHDV in one of the blowfly pools, confirming arthropods as an important vector for RHDV transmission. The implications of these findings will be presented.