Silene hifacensis is a narrowly endemic plant, restricted to a few small populations on limestone cliffs in the Spanish province of Alicante and on the Balearic island of Ibiza. The species was collected to extinction in its original mainland location by the early 20th century. Attempts have been made to reintroduce S. hifacensis to this area but conservation efforts are limited by a lack of information on the geographic structure of genetic variation in the species. We used nuclear (allozyme) and chloroplast DNA (cpDNA) PCR/RFLP markers to investigate the structure of genetic variation in 2 mainland and 6 Ibizan populations. Levels of allozyme variation were low, with a mean of 2 alleles per polymorphic locus. Mean (over polymorphic loci) total allozyme diversity (H-tot) was 0.203 and mean within-population diversity (H-pop) was 0.085. Most diversity was explained by the between-population diversity component (G(pop).reg = 57%). Both mainland populations showed allozyme fixation. Three composite cpDNA haplotypes were identified. The first is unique to a mainland population that is also allozymically distinct from all the other populations. The second haplotype is found in the other mainland population and one Ibizan population: these two populations are allozymically identical. The remaining Ibizan populations contain the third haplotype. The geographic distribution of allozymes and cpDNA haplotypes is discussed in terms of population history, dispersal and, speculatively, in terms of the possibility that there has been undocumented translocation of material between populations.