Pedunculate and sessile oaks (Quercus robur L.; Q. petraea [Matt] Liebl.) often coexist in mixed forest stands.
However, species-specific investigations and forest management actions in such populations require reliable
methods of identification of the species status of individuals. We investigated genetic diversity and species differentiation
of adult and naturally established seedling cohorts in a mixed forest stand composed of Q. robur and
Q. petraea, located in the Jamy Nature Reserve in north-central Poland. Using nineteen nuclear microsatellite
loci and a model-based clustering approach as a tool for species delineation, we efficiently identified 105 and
60 adults, as well as 191 and 456 seedlings of pedunculate and sessile oaks, respectively. While the adult trees
of both species were randomly distributed throughout the sample plot, the seedlings demonstrated significant
spatial clustering, which was particularly evident for Q. petraea. The two oak species exhibited similar levels of
genetic diversity in adult and offspring cohorts. Inbreeding was found to be low and significant only at the stage of
seedlings. The estimates of effective population size were higher for Q. robur than Q. petraea, despite the overall
greater reproductive success of the later one. There was a significant level of differentiation between the studied
oak species, as measured by Fst coefficient (0.084 – adults; 0.099 – seedlings). The results on genetic diversity and
species differentiation obtained in the studied indigenous near-natural stand of Q. robur and Q. petraea could be
considered as a reference for other population genetic studies of oaks.