Using nine chloroplast simple sequence repeats (cpSSRs) markers, we evaluated haplotypic variation within and among natural populations of Maritime pine (Pinus pinaster Ait.) in order to shed light on the history of this species. Seven out of the nine cpSSRs analysed were polymorphic, giving a total of 24 different variants. The 24 variants combined in 34 different haplotypes. The populations which generally showed the lowest level of haplotypic diversity are those located in Portugal. The Landes (France) and Pantelleria (Italy) populations represent the two main reservoirs of haplotypic diversity. The proportion of genetic differentiation among populations, estimated using R-st, which is a measure based upon a strict stepwise mutation model, was 0.235. The high level of differentiation was also confirmed by the AMOVA analysis (Phi(ST) = 0.254, P < 0.001). Four main groups of populations were identified on the basis of Principal Component Analysis, with the differences being statistically significant (Phi(CT) = 0.299, P < 0.001). Based on our results the presence of refugia located in the South of Portugal, previously proposed for this species, may be excluded? and a different possible recolonization process of Maritime pine in the post-glacial period has been proposed. Populations from North Africa and France might have represented a starting point of the recolonization process of Portugal and of the Italian part of the natural range, respectively. This hypothesis seems to be confirmed by the analysis of the distribution of the pairwise differences among individuals within populations: Landes and Pantelleria populations showed a bimodal distribution, as would be expected for ancient gene pools
