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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. 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 F₁ hybrids with a low incidence of backcrossing. Most of the post-F₁ 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.