tComparative analysis of chloroplast DNA (cpDNA) between two endemic moth orchids in Taiwan, Pha-laenopsis aphrodite subsp. formosana and P. equestris, previously revealed many evolutionary hotspots. Inthis study, we explored 27 pre-screened cpDNA regions to evaluate molecular markers for distinguishingPhalaenopsis species. Fifteen cpDNA markers were highly variable among moth orchids, with polymor-phic information contents ≥8.0. The rps16-trnQ marker showed the best discrimatory power which 15endemic moth orchids could be successfully separated into 13 groups. From the sequences of the sevenselected cpDNA regions, the rps16-trnQ intergenic spacer was the best DNA barcode which 19 endemicmoth orchids could be completely distinguished. The petN-psbM intergenic spacer could be better usedas a DNA barcode to differentiate P. aphrodite subsp. formosana and P. amabilis. Additionally, the inher-itance mode of cpDNA in moth orchids was maternally predominated. Phylogenetic analysis revealednon-monophyletic relationships below the Phalaenopsis genus level. In summary, we have revealed a setof cpDNA markers that could be used for identification and phylogenetic study of Phalaenopsis orchids.
