Infection of commercial garlic crops by viruses is common and substantially reduces crop quality and yield. Viruses found in garlic include members of the Poty-, Carla- and Allexivirus genera, and a Tospovirus, Iris yellow spot virus (IYSV). Virus spread in garlic crops is facilitated though vegetative propagation of infected bulbs, and through vectors, such as aphids, mites and thrips. Extensive international research has identified viruses infecting garlic, and their impacts on yield, however, there is limited knowledge for Australian garlic. This study evaluates the distribution of viruses in Australian field garlic and vegetative planting material across multiple growing districts located in Queensland, New South Wales, South Australia, and Victoria. Molecular screening of crop samples was carried out using genus-specific RT-PCR-based assays, followed by species-specific hybridisation assays. The samples were tested for three potyviruses, Onion yellow dwarf virus (OYDV), Shallot yellow strip virus (SYSV), and Leek yellow stripe virus (LYSV), three carlaviruses, Garlic common latent virus (GarCLV), Garlic latent virus (GarLV) and Shallot latent virus (SLV), and five allexiviruses, Garlic viruses A, B, C and X (GarVA, -B, -C, and –X) and Shallot virus X (ShVX). Virus incidence within planting material was near 100%, with plants carrying at least one virus from each of the three genera tested. The most common infections were potyviruses, OYDV and LYSV, and carlaviruses, SLV and GarCLV. The genetic diversity of local viruses was evaluated through sequencing of the viral coat protein (CP) across a selection of isolates. Increased knowledge of virus population dynamics in Australian crops, their vectors and weed hosts, contributes to our understanding of virus epidemiology and supports quarantine efforts attempting to limit the entry and spread of new viruses into Australia. Additionally, this study supports further development of virus free garlic germplasm in Australia and contributes targeted pest management strategies for industry.