Oaks are model species for the study of natural introgressive hybridization. High interfertility among oak taxa might result in collective evolution, through transpecific spread of advantageous alleles, challenging the standard concept of species. Nine highly polymorphic microsatellite (nuSSR) loci were analysed in three mixed oak populations of Quercus pyrenaica and Quercus petraea (Montejo, Somosierra and Robregordo) with different density and hybridization rates. Both leaf morphology and molecular markers were used to assess individual admixture rates. Insights about the relative effect of density and hybridization rates on fine-scale spatial genetic structure (SGS) were obtained from autocorrelograms and Sp statistics. Differences in SGS among populations were higher than between species. These differences cannot be attributed solely to census densities but also relate to other factors, such as the spatial configuration of the population. Hybridization was an important factor shaping within-population spatial genetic structure, and an interspecific component of SGS was found in Somosierra. Indirect estimates of historical gene flow in Montejo were compared with actual values of gene dispersal assessed by parentage analysis in a former study. Similar values were found for current and historical gene flow in both species, which might reflect demographical stability.