Hybridisation is a complex process that has important evolutionary consequences. In the case of rare species, a comprehensive understanding of inter-specific hybridisation can be critical for their conservation and management. Eucalyptus tetrapleura is a rare species of ironbark that is restricted to a 40 km × 100 km area around Grafton on the North Coast of New South Wales (Australia), and is distinctive in that it has four ribs on the sides of its buds and fruits. In recent years, central populations of E. tetrapleura have been cleared to facilitate upgrades to one of the major highways in eastern Australia. This has led to increased habitat fragmentation, and there are now concerns that the species is at risk of genetic swamping by more common ironbark relatives. In this study, we investigated the population genetics and patterns of gene flow in E. tetrapleura. We used DArTseq to genotype samples collected from across the known distribution of E. tetrapleura, as well as leaf material collected from co-occurring ironbark species. We found that while E. tetrapleura was a distinct evolutionary lineage, there was evidence of gene flow between this species and other ironbarks. Furthermore, many populations that had been identified as E. tetrapleura on the basis of morphology were of hybrid origin, thus the range of the species was much smaller than previously thought. Overall, our findings demonstrate how genomic methods can improve our understanding of admixture across closely related lineages, which can be used to inform the restoration of rare species.