<p>The origin of narrow endemic plants is a long-standing issue in Mediterranean biogeography. Estimates of divergence time may provide new insights into the likely pivotal periods in the evolutionary history of narrow endemics. Here, based on transcriptomic data and benefiting from the phylogenomic data provided by the Plant and Fungal Trees of Life Project (PAFTOL), we examined the origin of the narrow endemic plant <i>Arenaria provincialis</i>. We used several nuclear and plastid loci to conduct divergence time analyses embracing uncertainty of node age calibrations, allowing us to provide a new time tree for the plastid lineages of this species. The results clearly support a deep divergence time within <i>A. provincialis</i> that likely occurred during the Pliocene. This timeline shows that the evolutionary history of <i>A. provincialis</i> is closely linked to the geological and climatic changes that shaped the massifs of Provence (southeast France) before the Pleistocene. Our study also illustrates the contribution of the open and comprehensive PAFTOL project to divergence time analyses.</p>