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The taxonomic position of Castanopsis longzhouica C. C. Huang & Y. T. Chang has been controversial. Various authors included it in Castanopsis (D. Don) Spach, or Lithocarpus Bl. based on morphology, palynology and wood anatomy. In order to investigate this issue, sequences of nuclear ITS and the chloroplast genes matK and trnL-F of C. longzhouica were analyzed together with 72 representatives of 7 genera within Fagaceae. As for species of Lithocarpus, there were a 1-bp insertion and two unique 3-bp deletions from ITS2 of C. longzhouica distinguishing it from Castanopsis. The phylogenetic analyses on the separate ITS data and the joint data (ITS+matK+ trnL-F) strongly supported a derived position of C. longzhouica within a clade consisting of members of Lithocarpus. The result is consistent with previous suggestions based on wood anatomy, suggesting that C. longzhouica should be transferred to Lithocarpus. In addition, the shallow cup-shaped, loose incoherent-scale and indehiscent cupule and the concave scar of C. longzhouica suggests a close relationship to species of Lithocarpus. Based on these data, the new combination Lithocarpus longzhouicus (C. C. Huang & Y. T. Chang) J. Q. Li & L. Chen is proposed.