In 2011 a population of Grey-headed flying foxes (GHFF, Pteropus poliocephalus) set up camp in Adelaide’s Botanic Park. This population has grown to more than 36,000 and direct or indirect contact of these animals with humans is increasing. Flying foxes (FFs) act as reservoirs for viruses that have the potential to be transmitted to humans, domesticated animals or livestock. It is therefore important to define the viral species circulating within this GHFF colony to determine their biosecurity risk. We sampled faeces (230 Samples) and urine (24 samples) from the GHFF camp, extracted RNA, generated cDNA and amplified this using a single primer sequence independent amplification (SISPA) protocol. The resultant DNA samples underwent Nextera library preparation (Faecal = 23 libraries, 10/library; Urine = 12 libraries, 2/library) for paired end sequencing on a NOVASEQ 6000. These libraries generated on average 17 million or 11 million reads per library for faecal and urine samples respectively. Sequencing reads were trimmed and reads from samples of the same type were pooled for de novo meta-assembly of contigs using CLC Genomics. This generated 197,409 contigs from all the faecal samples, and 161,336 contigs from all the urine samples. Kraken2 taxonomic classification of contigs was carried out, resulting in 9188 contigs classified as viral in the fecal samples and 2728 classified as viral in the urine samples. Herpesvirales had the highest numbers of contigs classified of any viral order in both urine (340) and faecal (840) assemblies. Contigs for Retroviridae, Poxviridae, and Coronaviridae were also found in the samples. Further analysis of the reads and contigs generated will enable us to more closely scrutinize the viral species present, arming us with knowledge and information to be proactive in protecting the health of both human and animal populations.