Mosquito-borne flaviviruses are responsible for significant diseases, such as dengue fever, Japanese encephalitis, West Nile fever, and Zika fever. However, a subgroup of flaviviruses known as insect-specific flavivirus (ISFs) are only found in mosquitoes and do not infect or replicate in vertebrates. ISFs are of particular interest due to their intriguing evolutionary origins and growing evidence that they can interfere with the transmission of some flavivirus pathogens. Moreover, they can provide the platform for the development of safe diagnostics and vaccines for flaviviral diseases. In this project, the biodiversity of ISFs in northern Australia was investigated using a novel broad-spectrum, sequence-independent virus screening system in addition to a pan-flavivirus RT-PCR. New flaviviruses were further characterised through deep sequencing, phylogenetic and antigenic analyses as well as infection studies in a range of vertebrate and mosquito cell lines. Two novel ISFs, tentatively named Binjari virus (BinJV) and Lily Creek virus (LiCV) were detected in and isolated from Aedes normanensis and Aedeomyia catasticta mosquitoes, respectively. Analysis of the full-length genome sequence of the new viruses revealed they were phylogenetically distinct from all other flaviviruses reported to date, but were most closely related to Lineage II ISFs. Monoclonal antibody binding profiles further revealed that BinJV and LiCV were antigenically distinct from other flaviviruses. Development of infectious DNAs of wild type and mutant BinJV as well as chimeric viruses formed between BinJV and West Nile, Zika or dengue virus provides a novel recombinant vehicle for efficient production of safe, next-generation flavivirus diagnostic antigens.