The present study compares the species classification of pedunculate and sessile oaks (Quercus robur and Q. petraea) by means of leave traits and isozyme gene loci. Principal Component Analysis is applied as a method for species classification. At the population level, the classification is identical between both kinds of traits for all analysed populations. For single individuals, 85% of all trees are classified in the same way. The use of isozyme analysis in combination with Principal Component Analysis offers new possibilities for identification of locally adapted seeds and plant material, even when leave traits are not available. The genetic differentiation of both species is discussed in context with hybridisation and gene flow.