Pinus halepensis and P. brutia hybridize extensively.The analysis of monoterpenoid and morphological variability of 122 pine treesat five sites showed that the within-site heterogeneity is high while theentire provenance diversity is comparable with that of a circum-Mediterraneanscale. Four morphotypes and four chemotypes were recognized. The congruencebetween morphological and monoterpenoid classification of pines was high (coefficientof contingency 89%) while thirteen family groups of genetically closelyrelated trees were found by means of a specifically designed sampling schemeof continuous classification – identification and re-sampling. Putativehybrids contributed substantially to the observed diversity and there is considerableheterogeneity between sites. Low-altitude sites, presumably susceptible tosea-level fluctuations, alluvial deposition and human influence, are in generalmore diverse at both levels of genetic complexity than inland sites. The hybridphenotypes were not merely intermediate forms of parental taxa, and in a multivariatesense they are located on a parabola in the space of morphological properties.The arrangement of hybrids in the monoterpenoid space did not reveal any clear-cutpattern except that three major composite axes can summarize 98.9%of the entire monoterpenoid variation. The observed pattern of variation wasinterpreted as a result of waves of introgressive influence of eastern P. brutia population on P. halepensis, which was caused by marinetransgressions in Pliocene and eustatic sea-level fluctuations in Pleistocene.The human influence on this introgression accelerated the process, and amplifiedthe resulted pattern, although it blurred in many instances the biogeographicroutes of germplasm mixing. Its bearing on the evolution of pines is discussed,and it was found that the ‘Eocene refugia hypothesis’ of C.I.Millar holds by analogy also in central Aegean pines.