A new surveillance system will be discussed for the early detection of airborne Myrtle rust (Austropuccinia psidii), a serious fungal disease threatening many iconic Australian species. This system will deploy new generation air samplers and environmental monitoring devices within strategically chosen Botanic Gardens across Australia. Samples will be tracked from around the national network and undergo downstream molecular analysis to both quantify myrtle rust detections in the air by quantitative PCR and sequence the DNA to enable identification at the strain level and detect novel strains. Detection of strains of concern, first reported to the State and Federal agencies as per established biosecurity reporting protocols, will generate valuable data to national coordinated approaches that address the risks posed by myrtle Rust, including community action and engagement to prevent spread and raise awareness. The systems will also provide completely new epidemiological insights that are important for long-term conservation strategies of many threatened species, currently housed in Botanic Gardens. Linkage to the Gardens also capitalises on on-ground expertise to link airborne detections to these unique sites for symptom scouting of disease outbreaks. The project team will report activities to a website to promote these novel strategies and to visualise the dynamics of airborne myrtle rust at each site using a data dashboard. This aims to enhance pathogen surveillance data available to these valuable custodians of Australia’s living plant collections, but also inform plant conservation experts and special interest groups tasked with improving the long-term management strategies for myrtle rust in Australian regions with both new and established infections. This project, supported by the Australian Government Saving Native Species Program within the Department of Climate Change, Energy, the Environment, and Water (DEECCW), is a collaboration between plant health surveillance systems and commercialised molecular diagnostic pipelines at SARDI, innovative automation technologies and data management systems at Data Effects, and cutting-edge molecular plant pathology techniques at ANU School of Biology.