| Summary: | A hybrid origin for a conservation listed taxon will influence its status and management options. Here, we investigate the genetic origins of a nationally endangered listed taxon—<i>Eucalyptus paludicola</i>—a tree that is restricted to the Fleurieu Peninsula and Kangaroo Island of South Australia. Since its description in 1995, there have been suggestions that this taxon may potentially be a stable hybrid species<i>.</i> Using a high throughput sequencing approach, we developed a panel of polymorphic loci that were screened across <i>E. paludicola </i>and its putative parental species <i>E. cosmophylla </i>and <i>E. ovata. </i>Bayesian clustering of the genotype data identified separate groups comprising <i>E. ovata </i>and <i>E. cosmophylla </i>while <i>E. paludicola </i>individuals were admixed between these two, consistent with a hybrid origin. Hybrid class assignment tests indicate that the majority of <i>E. paludicola </i>individuals (~70%) are F<sub>1</sub> hybrids with a low incidence of backcrossing<i>. </i>Most of the post-F<sub>1 </sub>hybrids were associated with revegetation sites suggesting they may be maladapted and rarely reach maturity under natural conditions. These data support the hypothesis that <i>E. paludicola </i>is a transient hybrid entity rather than a distinct hybrid species. We briefly discuss the conservation implications of our findings.
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