Castrilanthemum debeauxii is a critically endangered annual plant narrowly distributed in mountains of SE Iberia. It occurs in spiny scrublands on limestone soils dominated by Erinacea anthyllis at medium altitudes. Phylogenetic results indicate that the monotypic Castrilanthemum constitutes a paleoendemic lineage that diverged from its closest extant relatives in the Miocene. To achieve a better understanding of its recent evolution and conservation status, we performed an analysis of genetic variation and structure of four subpopulations using plastid haplotypes and AFLPs. We also investigated additional characteristics (ecological requirements, reproductive biology, pre-dispersal seed predation) that are relevant to evaluate the conservation status of the species. Castrilanthemum was found to be a facultative selfer with no major germination limitations. We detected moderate levels of genetic diversity based on AFLPs and plastid DNA sequences. The low genetic structure found for both nuclear and plastid markers, together with species distribution modeling results, pointed to high gene flow, which might counteract processes of genetic erosion caused by the low number of individuals. We found significant levels of pre-dispersal seed predation by the burrowing larvae of a tephritid fly, which may have contributed to the decline of the populations. Based on our results, we suggest directions for the management of Castrilanthemum. In particular, we recommend seeding and collection of seeds for banks, and discuss the possibilities of population reinforcement and reintroduction in localities where the species is currently extinct.