Forest fragmentation induced by urbanization usually has a negative effect on gene flow by limiting animal-mediated seed dispersal. Since the effect of forest fragmentation on animal-induced seed dispersal is related to seed size, it is likely that the impact of such fragmentation on genetic structure varies among the species with different seed sizes. To test this prediction, we investigated the genetic diversity, structure and kinship structure of seedlings and adult trees in two different seed-sized oaks, Quercus variabilis and Quercus chenii, which are undergoing seed dispersal limitation in urban areas, e.g. Wuhan city, a rapidly urbanizing megacity in central China. Compared to the large-seeded oak Q. variabilis, more full-sibling and maternal-offspring pairs of the small-seeded oak Q. chenii were detected among and within forest patches, indicating small-seeded species was enduring less restricted seed-mediated gene flow than large-seeded species in urban areas. For both oaks, genetic differentiation of seedlings mainly occurred within populations instead of among populations, and more half-siblings than full-sibling pairs and more paternal-offspring than maternal-offspring pairs were observed. In addition, genetic diversity within forests was positively associated with population size. The results indicate frequent gene flow of oaks, mainly from wind pollination, exists among urban forest patches and then offsets the reductions of gene flow from seed dispersal. Our results suggest that wind-pollinated and animal-dispersal small-seeded species, might suffer from less limitation of gene flow in fragmented urban forests, thus they can be candidates for urban greening and planting. In addition, enhancing habitat connectivity and maintaining large populations are also essential to promote gene flow and preserve genetic diversity.