Background and aims – It is a key conservation aim to maintain genetic diversity within populations of rare and threatened species. The flora of the Sinai Peninsula is unique and, therefore, of strong interest. However, in only few studies genetic structure and variation within and among populations of Sinai plants have been analysed. In the study presented here, we analysed the genetic structure of Hypericum sinaicum and Origanum syriacum subsp. sinaicum, which are two rare respectively near-endemic and endemic medicinal perennial plants with overlapping ranges restricted to the mountainous region of southern Sinai in Egypt. Methods and key results – We used AFLP markers and calculated standard genetic diversity measures. Both species exhibited much higher genetic diversity and lower genetic differentiation than generally reported for endemic plants. Although the taxa differed in distribution range and density of populations in the study region (local scale), molecular variation within populations was not significantly different between both taxa. H. sinaicum, the taxon with the narrower range and fewer populations, exhibited a stronger population differentiation than O. syriacum subsp. sinaicum, the taxon with the wider range and more populations at the scale of the study. Populations of both species followed the isolation-by-distance model. Bayesian clustering of individuals was successful in identifying several populations with distinct gene pools in both taxa. Conclusions – We discussed recommendations for conservation of each taxon and concluded that the conservation of genetic diversity occurring naturally in these taxa should still be possible by a combination of in situ and ex situ conservation efforts.

AFLPS; CONSERVATION GENETICS; HYPERICACEAE; LAMIACEAE; MEDICINAL PLANTS; SINAI