The genetic variation and structure of Sladenia celastrifolia Kurz, a species of conservation concern, were investigated. Analyses of two chloroplast DNA loci (trnS-trnG and atpB-rbcL intergenic regions) were carried out for 24 populations of S. celastrifolia and five haplotypes were identified. High levels of genetic differentiation (GST = 1, FST = 1) were detected, which may be a result of limited gene flow caused by geographic isolation. Analysis of molecular variance suggests that the existence of marked phylogeographical structure within the haplotype distribution is probably due to geographic barriers among populations. The haplotype network and mismatch distribution analyses did not detect any signals for recent population expansions in S. celastrifolia. Thus, it can be inferred that the species likely persisted in situ during climatic oscillations. Considering its genetic diversity and uniqueness, conservation strategies are further discussed for this species.