Fagus sylvatica L. is one of the most widespread broad-leaved trees in the temperate forests of the northern hemisphere. In addition to two subspecies, F. sylvatica ssp. sylvatica in Europe and F. sylvatica ssp. orientalis in south-western Asia, two further taxa were described: F. moesiaca (Maly) Czeczott in the south-western Balkans and F. taurica Popl. in Crimea. The opinions about the number and ranks of taxa within this complex are highly controversial. To assess the degree of genetic differentiation among them, and to reveal geographical patterns of genetic diversity and their relationships to history and biogeography of beech populations, genetic variation at 12 allozyme loci was studied in 279 populations in western Eurasia. A Bayesian analysis of population structure revealed the existence of two clusters, which fairly well coincided with F. sylvatica ssp. sylvatica and F. sylvatica ssp. orientalis, whereby the populations from the south-western Balkans and Crimea contained a mixture of these two gene pools. On the other hand, a neighbour-joining tree based on pairwise FST failed to separate the subspecies into well-defined distinct clades. Populations of F. sylvatica ssp. orientalis proved to be incomparably more differentiated than ssp. sylvatica (FST = 0.157 and 0.032, respectively). Asian populations also showed higher levels of allelic richness both on population and taxon levels than the European ones (the number of alleles after rarefaction was 3.40 and 4.27 in F. sylvatica ssp. sylvatica and ssp. orientalis, respectively). This indicates that the gene pool of F. sylvatica ssp. orientalis has not been depleted by reduced population sizes during the Pleistocene glaciations, as is the case of F. sylvatica ssp. sylvatica. Genetic similarities between isolated regional populations are explained by shared ancestral polymorphisms and/or range overlaps with subsequent hybridization in the past. © 2007 The Linnean Society of London, Botanical Journal of the Linnean Society, 2007, 154, 165–174.