Abstract: Dipteronia dyerana is one of the endangered species of genus Dipteronia, and its phylogenetic placement is still in dispute thus far. To access the systematic placement of D. dyerana, the sequences of ITS, CHS, psbM-trnD spacer, rbcL, trnD-trnT spacer, rpl16 intron, trnL-trnF spacer and psbA-trnH spacer regions from the target species were analyzed using parsimony and Bayesian inference methods. The results showed that: 1) The Dipteronia was a monophyletic lineage in six chloroplast DNA genes combined. 2) In CHS, Dipteronia was a monophyletic lineage, but had a fuzzy relationship with Acer spp. 3) D. dyerana nested in Acer and Dipteronia was a paraphyletic lineage in ITS. These results indicated that different data sets had a conflict result, it may be due to different rates of each gene fragment evolution. Less informative sites in CHS and the multicopy in ITS may be the reason why they have different result with six chloroplast DNA genes combined. Integrated research results and morphological evidence, systematic placement of D. dyerana should belong to Dipteronia. Moreover, much more genes should be chosen when study on systematic placement of D. dyerana.