Abstract:In order to explore the causes of the endangered species Horsfieldia hainanensis, the genetic diversity and population structure were analyzed by using restriction-site associated DNA sequencing (RAD-seq) for developing single nucleotide polymorphisms (SNPs). The results showed that the genetic diversity of H. hainanensis was low (Ho=0.167) and the genetic differentiation between populations was significant (Fst=0.120). Structure analysis showed that the optimal clustering value of the population was 2, but the genetic structure of some populations was mixed, which was consistent with the results of Mantel correlation test showing no correlation between genetic distance and geographic distance (r=0.733, P<0.075). Therefore, low regeneration ability and excessive disturbance of human activities might be the main reason for endangered status of H. hainanensis. It was recommended to strengthen in situ conservation of populations with high genetic diversity, such as BWL and YGL, and strengthen near-situ or ex-situ conservation of populations with severe habitat damage, such as EXL and DLS, to increase gene exchange among populations. At the same time construct the core germplasm of this species to prevent the aggravation of genetic resource loss.