This species is scarce in its natural habitat and is assessed as endangered according to the IUCN Red List of Threatened Species (Ly et al., 2018). The remaining population of H. hainanensis is severely fragmented and isolated in a few reserves in Hainan Island. As a result, adult trees of this species had been overly logged, leading to a reduction of 50%–70% population in the last three hundred years (Ly et al., 2018). Hopea hainanensis is known for its highly valued timber which is extremely durable and suitable for making boats and building bridges and houses (Li et al., 2007). It is found in tropical lowland forest of Hainan Island and northern Vietnam (Li et al., 2007). Hopea hainanensis Merrill & Chun is a large evergreen tree that can grow up to 20 m. The 12 polymorphic microsatellite markers could be applied to study genetic diversity, population differentiation, mating system, and fine‐scale spatial genetic structures of H. hainanensis as well as its close relatives, facilitating the conservation and restoration of these endangered but valuable Hopea species. A neighbor joining dendrogram clustered all individuals into two major groups, one of which was exclusively constituted by H. hainanensis, while the other consisted of two subgroups, corresponding to H. reticulata and H. chinensis, respectively. The results showed that H. reticulata and H. hainanensis had similar levels of genetic diversity. and Hopea reticulata Tardieu, in which 3 and 7 microsatellite markers were found to be polymorphic, separately. Primer transferability was tested with Hopea chinensis Hand.‐Mazz. GENODIVE analyses indicated that the number of alleles ranged from 2 to 6 per locus, and the observed and expected heterozygosity varied from 0 to 0.755 and from 0.259 to 0.779, respectively. Twelve markers were found to be polymorphic in H. hainanensis. Twenty‐six microsatellite markers were developed based on next‐generation sequencing data and were genotyped by capillary electrophoresis on an ABI 3730xl DNA Analyzer. Microsatellite markers were isolated and characterized for Hopea hainanensis Merrill & Chun, an endangered tree species with scattered distribution in Hainan Island and northern Vietnam.
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