Asian (sub)tropical karst regions harbor high endemism and species diversity of sclerophyllous oaks. In this study, Quercus zhekunii, a new species from Guangxi, China, is described and illustrated. Phylogenomic reconstruction using RAD-seq placed this new species within the “Tropical Clade” of Quercus sect. Ilex. The dense fused fasciculate and uniserate trichomes on the leaf abaxial surface of Q. zhekunii resemble those of Q. kingiana. However, its distinctively concave primary and lateral veins on the leaf adaxial surface, along with the prominent backward-recurved leaf blade and leaf margin, make it morphologically distinct from any known species in Q. sect. Ilex. The conservation status of Q. zhekunii is assessed as Endangered (EN). A new identification key to the species in the “Tropical Clade” is provided. In addition, character evolution and phylogeography of the “Tropical Clade” of Q. sect. Ilex is briefly discussed based on the new phylogenetic and morpho-anatomical data.