Molecular phylogenetic analyses using two data sets, derived from DNA sequences of matK, the maturase-encoding gene located in an intron of the chloroplast gene trnK, and ITS (internal transcribed spacer) region of the 18S-26S nuclear ribosomal DNA, were performed to examine relationships among 37 taxa in Cymbidium. Although each data set did not provide conclusive evidence in itself, the data sets combining the two regions yielded the following insights: (1) Cymbidium subgenus Cyperorchis and section Pachyrhizanthe, often treated as independent genera, were nested within the remaining members of Cymbidium. (2) All the three subgenera of Cymbidium, namely, Cymbidium, Cyperorchis, and Jensoa, turned to be para-/polyphyletic. (3) Among sections of Cymbidium, Austrocymbidium, Cyperorchis, Iridorchis, and Maxillarianthe did not show monophyly. (4) At specific level, our results indicated the polyphyly of Cymbidium bicolor, although bootstrap supports for the clades including C. bicolor were not robust.