1. Understanding how invasive species respond to novel environments is limited by a lack of sensitivity and throughput in conventional biomonitoring methods. Arthropods in particular are often difficult to monitor due to small size, rapid lifecycles, and/or visual similarities with co-occurring species. This is true for the agromyzid leafminer, Liriomyza sativae, a global pest of vegetable and nursery industries that has recently established in Australia. 2. A highly robust method based on environmental DNA (eDNA) was developed exploiting traces of DNA left inside ‘empty’ leaf mines, which are easier to collect and persist longer in the environment than the insect. This extended the window of possible diagnosis to at least 28 days since a leaf mine became empty. The test allowed for visually indistinguishable leafmining damage caused by L. sativae to be genetically differentiated from that of other flies. 3. Field application resulted in the identification of new local plant hosts for L. sativae, including widely distributed weeds and common garden crops, with important implications for the pest’s ability to spread. Moreover, the test allowed for the confirmation of L. sativae on an island with a previously unconfirmed population. 4. The developed eDNA method is likely to become an important tool for L. sativae and other leafmining species of biosecurity significance, which, historically, have been difficult to detect, diagnose and monitor. More generally, eDNA is emerging as a highly sensitive and labour-efficient surveillance tool for difficult to survey species to improve outcomes for agricultural industries, global health, and the environment.