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Myrtle rust, caused by the pathogen Austropuccinia psidii, is a disease affecting numerous species of Myrtaceae around the globe. Many Australian ecosystems are dominated by Myrtaceae, making them, along with the industries that rely on them, particularly vulnerable to this disease. With over 800 endemic species, Eucalyptus is a major genus within the Myrtaceae in Australia. Wide variation in response to A. psidii infection, from extreme susceptibility to resistance, has been reported among Eucalyptus species in which any pre-formed resistance to this invasive pathogen is unexpected. This study aims to define and contrast geographical patterns of variation in rust susceptibility within the overlapping, natural ranges of Eucalyptus globulus and Eucalyptus obliqua, two commercially and ecologically important species from different Eucalyptus subgenera. Phenotypic disease screening of seedlings of E. globulus races and E. obliqua forest districts (defined geographically) showed E. obliqua to be more susceptible than E. globulus with significant differences in disease susceptibility and symptomatic trait expression. Eucalyptus globulus showed a trend for decreased susceptibility to A. psidii from south- to north-eastern Tasmania, eastwards along the Otway Ranges and southward from the Strzelecki Ranges to the Wilson Promontory Lighthouse in Victoria, but no such geographical patterns were observed within E. obliqua. No significant correlations were found between climatic conditions (i.e. rainfall, temperature and elevation) and rust susceptibility at provenance levels in either species. Taken together, these results support a hypothesis that population divergence in resistance to A. psidii has not been driven by climate.