| Summary: | Genetic diversity and the extent of clonality in a plant species can significantly influence its reproductive success. Whilst clonality can be an effective life-history strategy, in harsh environments it can lead to low levels of diversity and sexual reproductive failure. <i>Santalum lanceolatum</i> (Santalaceae) is a hemi-parasitic shrub endemic to the monsoonal dry tropics of northern Australia, which was harvested for its oil-rich heartwood from natural populations in Cape York, Australia. Despite wild harvesting ending over 70 years ago, populations in the region are currently declining. The aims of this study were to examine genetic variation, population genetic structure, inbreeding and clonality of six <i>S. lanceolatum</i> populations from this northern margin of the species range. Analyses of twelve microsatellite markers showed <i>S. lanceolatum</i> had low genetic diversity (<i>A<sub>R</sub></i> = 2.776, <i>H<sub>E</sub></i> = 0.409), evidence of regional differentiation (<i>F<sub>ST</sub></i> = 0.307–0.424) and negligible inbreeding levels (<i>F</i> = −0.052). Clonality investigations revealed 135 genets among 200 samples, suggesting that the clonal structure of <i>S. lanceolatum</i> may be limiting the potential for sexual reproduction and natural recruitment. We recommend a conservation strategy involving genetic rescue to prevent the further decline and potential local extinction from a variety of environmental pressures and human activities.
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