Sessile oak (Quercus petraea) and pedunculate oak (Q. robur) are two closely related, interfertile taxa. They are the most frequent oak species in Switzerland. Allelic and genotypic structures at 17 isozyme gene loci were observed in 21 populations from Switzerland. Twelve populations of Q. petraea, six populations of Q. robur, and three "mixed" populations (Q. petraea and Q. robur) were investigated. The species status of the populations was confirmed by Principal Component Analysis (PCA) based on leaf morphological traits. All populations are highly variable at enzyme gene loci. Differentiation among the taxa is reflected at allelic structures at several enzyme gene loci (ACP-C, GDH-A, IDH-B, NDH-A, PGM-A). An excess of homozygotes relative to corresponding HARDY-WEINBERG structures was observed in all populations. Moderate levels of inbreeding are likely to contribute to these genotypic structures, but heterogeneity of inbreeding coefficients among loci suggests that deviations from random mating are not the only cause of the homozygote excess at particular loci (AAP-A, PGM-A). On average, expected heterozygosity is highest in the "mixed" populations, but observed heterozygosity of the "mixed" stands is in-between Q. petraea and Q. robur. A plausible explanation is partial reproductive isolation of both species in "mixed" forests resulting in a "Wahlund effect". Seed procurement in "mixed" oak forests is encouraged. The species status of populations is of prime importance for the selection of oak genetic resources in Switzerland.