Pinus halepensis and P. brutia hybridize extensively. The analysis of monoterpenoid and morphological variability of 122 pine trees at five sites showed that the within-site heterogeneity is high while the entire provenance diversity is comparable with that of a circum-Mediterranean scale. Four morphotypes and four chemotypes were recognized. The congruence between morphological and monoterpenoid classification of pines was high (coefficient of contingency 89%) while thirteen family groups of genetically closely related trees were found by means of a specifically designed sampling scheme of continuous classification – identification and re-sampling. Putative hybrids contributed substantially to the observed diversity and there is considerable heterogeneity between sites. Low-altitude sites, presumably susceptible to sea-level fluctuations, alluvial deposition and human influence, are in general more diverse at both levels of genetic complexity than inland sites. The hybrid phenotypes were not merely intermediate forms of parental taxa, and in a multivariate sense 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-cut pattern except that three major composite axes can summarize 98.9% of the entire monoterpenoid variation. The observed pattern of variation was interpreted as a result of waves of introgressive influence of eastern P. brutia population on P. halepensis, which was caused by marine transgressions in Pliocene and eustatic sea-level fluctuations in Pleistocene. The human influence on this introgression accelerated the process, and amplified the resulted pattern, although it blurred in many instances the biogeographic routes 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.