The high species diversity and endemism of the Maritime Alps suggest that this region may have held several refugia during the Pleistocene glaciations. Nevertheless, this assumption has rarely been examined. Here we investigate the genetic diversity of Saxifraga florulenta, a rare endemic restricted to siliceous substrates in the Maritime Alps. Overlaying the maximum extension of the ice sheet during the Pleistocene, the current distributions of S. florulenta and siliceous substrates suggest the existence of two putative refugial areas in the Maritime Alps. By using evidence from amplified fragment length polymorphisms we aim at elucidating whether genetic structure of the species corresponds to this two-refugia hypothesis and how this genetic information can be used to ensure its long-term conservation. Low levels of species-wide and within-population genetic diversity were detected, suggesting strong historical bottlenecks. Bayesian and principal coordinate analyses identified two population groups in agreement with the two refugia hypothesis. However, weak genetic divergence between these groups suggests that their separation happened more recently, and that S. florulenta survived the Pleistocene glaciations in one main refugium. The lack of a significant correlation among genetic and geographic distances implies that populations are not at migration-drift equilibrium and current levels of gene flow among them do not appear to be sufficient to balance the effect of genetic drift. Hence, in future conservation strategies, special care should be taken to preserve both gene pools and prevent further fragmentation of populations.