Reproductive isolation between related oak species within one taxonomic section is incomplete. Even though pre- and post-zygotic isolation mechanisms have been described for interfertile oak species, natural hybridization is common in contact zones between related oaks. The apparent restriction of inter-specific hybrids between ecologically divergent species to intermediate environments in contact zones suggests postzygotic isolation via environmental selection against hybrids in parental environments. Overrepresentation of hybrids in seeds as compared to adult trees provides additional indirect evidence for selection against hybrids. Here, we used genetic assignment analyses in progeny obtained from a sympatric stand of Quercus rubra and Quercus ellipsoidalis, two interfertile species with different adaptations to drought, to characterize the number of hybrids and “pure” species in the non-germinated acorns and in seedlings. The occurrence of 43.6 % F1 hybrids and introgressive forms among the non-germinated acorns and their very low frequency in the seedlings (9.3 %) is to our knowledge the first direct evidence for early selection against hybrids in oaks possibly as result of genetic incompatibilities. Additionally, we found a signature of positive selection on EST-SSR PIE200 in Q. rubra which needs further confirmation. These results contribute to our understanding of reproductive isolation and divergence between interfertile oak species with different ecological adaptations
