<p>Hybridization is a common phenomenon in plants, contributing to various outcomes that impact genetic diversity and species dynamics. To delve into these effects, we focused on four oak species: <i>Quercus acutissima</i>, <i>Q. variabilis</i>, <i>Q. fabri</i>, and <i>Q. serrata</i>. Using three genomic markers, we explored genetic diversity, hybrid identity, and introgression among these species. Our study revealed the high values of allelic richness, heterozygosity and number of private alleles for the populations investigated. Notably, gene flow is most active in the nuclear genome (<i>Nm</i>_nDNA = 4.82), followed by the chloroplast genome (<i>Nm</i>_cpDNA = 1.12), with the mitochondrial genome (<i>Nm</i>_mtDNA = 0.33) showing the most restricted gene flow. In the <i>Quercus</i> group, hybrids displayed higher genetic diversity and lower interspecific differentiation, particularly in nuclear and chloroplast genomes. Moreover, hybridization-induced leaf morphological variation further blurred species boundaries, complicating classification. In the <i>Cerris</i> group, asymmetric gene flow was observed, likely influenced by differences in pollen and seed dispersal abilities. This led to variations in the direction and intensity of gene flow among species. Our analysis identified various individual types, including purebreds and different generations of hybrids, all exhibiting hybrid vigor. Furthermore, our findings indicated that hybrid individuals possess phenotypic advantages, particularly in leaf width and leaf width to circumference ratio. These traits showed significant associations with environmental factors, notably longitude and latitude. Overall, our study highlights the importance of considering the effects of hybridization in oak forest conservation and taxonomy. We recommend further research to explore seed and pollen dispersal patterns through comprehensive genomic and landscape genetic analyses.</p>