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Oaks (<i>Quercus</i> spp.) are considered model plants for studying plant evolution and natural gene introgression. Beijing area is at the junction between Taihang Mountain and Yanshan Mountain, and it is an overlapping distribution area of several deciduous oaks native to China. Interspecific hybridization often occurs in sympatric sibling species, resulting in blurred interspecific boundaries and hindering the development of breeding. To have better improvement and protection of these oaks, it is urgently necessary to evaluate the genetic diversity and population structure of these oak species. In this study, we collected eleven populations of four oak species (<i>Q. variabilis</i>, <i>Q. mongolica</i>, <i>Q. dentata</i> and <i>Q. aliena</i>) in the Beijing area. By using the polymorphic SSR markers, we analyzed the genetic variation of the collected 400 individuals, investigated the population structure, and found gene introgression events. <i>Q. variabilis</i> had a clearer genetic background as compared to the other three species. <i>Q. mongolica</i> had a more frequent gene introgression with <i>Q. dentata</i> and <i>Q. aliena</i>. Our data reveal the introgression and genetic diversity of the four oak species native to the Beijing area, laying the foundation for conducting an oak germplasm nursery with a clear genetic background for protection and further improvement.