With the global biodiversity loss, it is crucial to protect the threatened species. While endemic species not only are important components of regional biodiversity, also the ecological niche of one has significant implication for ecosystem. The low genetic diversity of the endemic species is highly vulnerable to extinction. However, conservation of threatened or endemic species is relatively weak. It is urgent to formulate appropriate protection strategies. In this paper, based on chloroplast DNA sequencing, the 3,133 base pairs (bp) of combining 5 chloroplast genes (ycf13125-ycf14381, ycf11205-ycf12402, psbA-trnH, trnD-psbM and trnL-trnF) were analyzed from 6 populations of M. adenophora, a vulnerable and endemic tree growing in forests or at forest edges in China, detecting only 5 haplotypes with 4 polymorphic sites (0.13%). The total haplotype diversity (Hd) and nucleotide diversity (π) was 0.234 and 0.0001, respectively. It is shown that the extremely low genetic diversity in the species and thus 49 individuals shared common haplotype H1. The results of haplotype network, haplotype geographical distribution analysis and neutrality tests supported that populations had experienced recent expansion. The low genetic diversity values found in the present study raise considerable concern about the conservation status of M. adenophora and highlight the need to further protect genetic diversity to strengthen their resilience against further decline.