Clematis acerifolia is a critically endangered species endemic to an extremely narrow distribution range in Beijing Municipality. This species is often found on the vertical cliffs in gorges of Fangshan and Mentougou districts. Although most of the taxonomic treatments placed it into Sect. Cheiropsis, its systematic position has never been tested by the molecular evidence. To access the systematic position of C. acerifolia, sequences of the ITS, the plastid atpB-rbcL spacer, psbA-trnQ spacer and rpoB-trnC spacer regions from the whole genus were analyzed using parsimony and Bayesian inference methods. The results showed that: 1) relatively low resolution and support values were obtained in the separate analyses but were enhanced in the combined data analyses; 2) Clematis together with Naravelia formed a clade and these two genera should be merged; 3) traditionally taxonomic treatment of C. acerifolia was not supported and this species may not be a member of Sect. Cheiropsis; 4) the position of C. acerifolia was detected to be isolated in the genus and it may represent a relic species of Holarctic Clematis.