The genus Fagus (beech, Fagaceae) consists of about 10 species discontinuously distributed in East Asia, eastern North America, and Europe. Fagus multinervis occurs only on Ulleungdo Island, Korea, and is an important component of the island's plant community. The species was described primarily based on one of its stem characteristics: it branches at the base, producing several primary trunks. In part because no extant Fagus species are found in mainland Korea, and because the closest populations of Fagus are found in Japan, F. multinervis has been considered to be derived from the Japanese species, F. japonica. However, a recent study synonymized F. multinervis under F. engleriana and proposed that the beech population of Ulleungdo Island was derived instead from China via long-distance dispersal. Fagus multinervis is morphologically very similar to F. engleriana, but it can be distinguished by having rhombic lenticels that are vertically elongated. We determined the nucleotide sequences of the trnK-matK, trnL-trnF, trnH-psbA, and atpB-rbcL regions of plastid DNA and the second intron of the nuclear LEAFY gene from accessions of eight species, including eight F. multinervis individuals, in order to clarify the phylogenetic placement of this insular species. Phylogenetic analyses show that F. multinervis is monophyletic, and that it is closely related to F. engleriana and F. japonica. However, a sister relationship of F. multinervis with either of those species is not resolved. Therefore, our molecular data support the distinctness of F. multinervis as an endemic on Ulleungdo Island. Furthermore, incongruence between plastid and nuclear data suggests that F. multinervis may have originated via hybridization.