Genetic structure and genetic diversity in fourteen autochthonous populations of Pinus sylvestris L. from the Iberian peninsula and two populations from the Massif Central in France were studied at eleven isoenzymatic polymorphic loci. The studied populations formed two genetically similar but heterogeneous groups. The first group consist of populations localized in North-Eastern Spain with two genetically distinct populations. The second includes populations of the West-Central part of the Iberian peninsula. Populations from the Massif Central in France are diverse from those of Spain, but are similar to the group from North- part of the Iberian peninsula. The existence of significant numbers of private alleles in Spanish populations which were not observed in populations from the Massif Central, suggests that the Scots pine from the Iberian peninsula probably did not take part in the colonization of Europe after the last glaciations and represents original ancient tertiary gene pools.