The degree of clonality, interspecific hybridisation and inbreeding in rare species will have significant implications for maintenance of genetic diversity and resilience to environmental change, with related implications for immediate conservation management. Using microsatellites, we detected extensive clonality within the rare mallee, Eucalyptus absita, from a highly disturbed agricultural habitat in southwestern Australia. A total of just 16 unique genets, plus five putative hybrids with E. loxophleba, were detected across the known species range and these genets were estimated to be of considerable age. Each location possessed a unique genotype and overall diversity was moderate (H E = 0.547). The outcrossing rate in seedling progeny was low (t ₘ = 0.281), reflecting a rarity of intraspecific sires and minimal inbreeding depression prior to seed dispersal. Of all seedling progeny, up to 19 % were putative hybrids. Our findings indicate that despite rarity and clonality, moderate levels of genetic diversity and the capacity to produce outcrossed seeds is maintained. However, the ongoing maintenance of E. absita genetic diversity is significantly compromised by a high rate of selfing and potential hybridisation in seedling progeny. Seeds collected for long-term storage or rehabilitation should be screened for inbreeding and hybridisation rates to improve conservation outcomes. All existing adults represent a unique portion of the genepool for conservation.