Clonality and hybrid origin influence the conservation status of rare and restricted species. Eucalyptus bennettiae Carr & Carr is a rare species known only from a few individuals that may be clonal and may have arisen through hybridisation between other co-occurring species. The hybrid status and clonality of E. bennettiae was investigated with analysis of microsatellite variation in E. bennettiae compared with its putative parents, E. lehmannii subsp. parallela, E. sporadica and E. astringens subsp. redacta, identified through morphological characteristics. Analysis of microsatellite variation revealed clonality with one individual present at each location, and additivity of alleles and no unique alleles in E. bennettiae compared with two of the putative parents, E. lehmannii subsp. parallela and E. sporadica. In addition, E. bennettiae displayed intermediacy in species relationships and measures of relatedness, and assignment tests showed mixed ancestry in relation to these species but not the third putative parent, E. astringens subsp. redacta. These findings confirm that E. bennettiae is a hybrid and evaluation of the taxon for conservation protection shows that it does not satisfy the criteria for listing as a threatened species.