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Background and Aims The Mediterranean region is of prime importance to biodiversity at a global level, mainly due to the abundance of endemic plant species. However, information about these species is still scarce, especially at the genetic level. In this paper the first assessment is reported of the genetic structure of Centaurea horrida (Asteraceae), an endemic, sea-cliff-dwelling plant from Sardinia. Methods The study was conducted on seven populations covering the entire natural range of the species by means of SSR (microsatellite) markers. Key Results A considerable amount of genetic variation was found (average He = 0·603–0·854), together with a medium-high differentiation among populations, as estimated both by FST (0·123) and RST (0·158). Both Bayesian analysis and AMOVA were employed to detect genetic structuring in this species. The results suggest that the origins of the current populations of C. horrida lie in two gene pools. Conclusions Despite the restricted range, C. horrida displays high levels of genetic diversity, structured in such a way that three management units could be deemed viable for its conservation. The protected status of the species will probably suffice to prevent the impoverishment of its genetic resources. [ABSTRACT FROM AUTHOR]