Beschreibung:
<jats:title>Abstract</jats:title><jats:p><jats:italic>Fokienia hodginsii</jats:italic> is a Tertiary relict conifer of the monotypic genus <jats:italic>Fokienia</jats:italic> (Cupressaceae <jats:italic>s.l</jats:italic>.). Currently, the species is distributed in southern China, northern Vietnam, and northern Laos and listed as a “near threatened” species by the IUCN. In this study, a total of 427 individuals of <jats:italic>F. hodginsii</jats:italic> were sampled from China and Vietnam to characterize its genetic diversity and population differentiation. Based on the profiles of 12 simple sequence repeat (SSR) markers, we observed a high level of genetic diversity in <jats:italic>F. hodginsii</jats:italic> at the species level (<jats:italic>H</jats:italic><jats:sub>e</jats:sub> =0.635), albeit slightly lower than that of its sister species <jats:italic>Chamaecyparis obtusa</jats:italic>. Signals of bottleneck events were detected in the populations GXDMS, GXHJ, V‐PXB, and V‐HB, probably due to Pleistocene glaciations or overexploitation in recent years. Pronounced genetic differentiation (<jats:italic>F</jats:italic><jats:sub>st</jats:sub><jats:italic><jats:sub> </jats:sub></jats:italic>= 0.157) was found in this species. The inbreeding index (<jats:italic>F</jats:italic><jats:sub>is</jats:sub><jats:italic><jats:sub> </jats:sub>= </jats:italic>0.176 ± 0.024) indicated that <jats:italic>F. hodginsii</jats:italic> has a mixed mating system. Significant correlation was found between the pairwise genetic differentiation and geographic distance (<jats:italic>r</jats:italic> = 0.882, <jats:italic>p</jats:italic> = 0.01), suggesting that genetic differentiation among the populations follows the model of isolation by distance (IBD). STRUCTURE analysis and principal coordinate analysis revealed that these populations were divided into four groups: the western China group located mainly in the Yunnan–Guizhou Plateau, the central China group located mostly in the Luoxiao Mountains and Nanling Mountains, the eastern China group located in the Wuyi Mountains and the Vietnam group containing two populations in Vietnam. The different terrains and elevations of populations may be the most likely factors leading to the differentiation between the western China group and the central China group, while the geographic isolation caused by the lack of appropriate habitats may greatly contribute to the differentiation between the central China group and the eastern China group. Based on the results, some conservation suggestions for this species are provided, such as establishing seed orchards and multiple nature reserves.</jats:p>