The rocky habitats around the Mediterranean basin harbour many endemic plants. Geographical and ecological heterogeneities and past environmental changes of the Pleistocene are often proposed to explain the isolation and endemism of Mediterranean plant species. In this study we address the question of the endemism of Arenaria provincialis (Caryophyllaceae) an annual Mediterranean endemic plant restricted to the hills and modest calcareous mountains surrounding the city of Marseille. The results of a comparative study on the ecological niche and seed traits reveal that A. provincialis has a well-differentiated realized niche and diaspore. The inclusion of a phylogenetic analysis and a molecular dating approach allow us to propose an hypothetical scenario explaining the endemism of A. provincialis.