Based on morphological characters, the North African Silene patula has been divided into two subspecies,ssp. patula found North of Kabylies and Atlas Mountains, and ssp. amurensis found south of these regions. In order to test the hypothesis that S. patula could have derived from S. italica through the Sicilian Channel during the Messinian, we sequenced three chloroplast loci, trnH–psbA, trnS–trnG and rpl12–rps20. Fifteen haplotypes were found on 211 herbarium specimens, associated with a huge differentiation within species. The hypothesis that S. patula had independently evolved as two different subspecies North and South of the mountains is refuted and a morphological adaptation to different pollinators is suggested to explain the differences between the two taxa. The Kabylies–Numidie–Kroumirie gathers a large proportion of haplotypes, which points to this region as a probable refugium or place of origin from which spatial expansions have subsequently occurred towards Morocco and the Aurès Mountains.