Genetic variation determines the evolutionary potential of a species and is vital for fully understanding the evolution of a species, as well as for developing optimal conservation strategies. Horsfieldia tetratepala is classified as a Plant Species with Extremely Small Populations (PSESP) in China where it is an economically important rainforest tree, but it has declined sharply, mainly caused by habitat destruction and is now an endangered, narrow endemic. Effective conservation strategies for H. tetratepala are required urgently, but limited information exists about its genetic diversity. Accordingly, restriction site-associated DNA sequencing (RAD-seq) was used to sequence sixty-three H. tetratepala trees covering ten isolated populations to assess genomic diversity and population structure. The survey generated 8103 high-quality SNPs, analysis of which revealed low genetic diversity and moderate genetic differentiation among populations. However, Bayesian clustering of the sampled H. tetratepala populations produced two genetic clusters, though with some populations from Guangxi and Yunnan intermixed. Because of the increase in habitat fragmentation and human disturbance, conservation priority should be placed on populations with higher genetic variation (e.g., BB, TKH, DWS, and GLQ), allowing the formulation of more effective conservation strategies for this PSESP species.