Objective This paper clarifies the population structure and genetic diversity of rare and endangered plant Bretschneidera sinensis, so as to provide scientific basis for the formulation of effective conservation measures and management strategies.

Method According to the comprehensive investigation data of wild B. sinensis in Xianxialing Nature Reserve, Zhejiang Province of eastern China, the diameter class structure of B. sinensis was analyzed by static life table and survival curve. Sixteen samples were sequenced by gene recombination, and the nucleotide polymorphism, Tajima’s D value, observed heterozygosity and expected heterozygosity of Xianxialing population were calculated based on SNP markers.

Result (1) Based on the data of individual tree measurement data, the population of B. sinensis was divided into diameter class, the number of trees in diameter class Ⅰ was the most, and the population structure was generally increasing. (2) The nucleotide diversity of Xianxialing population was 0.000 155 ± 0.000 112, the average observed heterozygosity was 0.125 021, and the average expected heterozygosity was 0.251 483, which was lower than that of populations in other areas, and the genetic diversity within population was at a low level. (3) There was no significant correlation between population structure of growth type and genetic diversity.

Conclusion The diameter class structure of B. sinensis population in Xianxialing Nature Reserve is complete, and the number of B. sinensis population is increasing under the background of climate change in the future, but the level of genetic diversity is low. In the future, in the protection of rare and endangered species, we will actively carry out germplasm resource conservation to avoid population decline caused by the loss of genetic diversity.