Teak (Tectona grandis) has been widely planted in 70 tropical countries because of the utility and value of its wood. This species was introduced to Indonesia more than 100 years ago, and large plantations—covering 1.2 million ha—can be found on Java Island. However, little information currently exists about the genetic diversity and origin of these trees. We collected plant materials from three regions across Java Island (east, central, and west) and sampled trees spanning three age classes in each region, to clarify the genetic diversity and structure of teak plantations on Java Island. We investigated teak plantation and clonal experiment populations using multiplexed ISSR genotyping by sequencing (MIG-seq) and compared the genetic diversity and structure with the provenance test populations derived from natural teak forest in India, Myanmar, Thailand, and Laos. Analyses using 459 single-nucleotide polymorphism (SNP) loci revealed that native provenances had higher genetic diversity than the Indonesian teak plantations. Moreover, old teak plantations demonstrated lower genetic diversity than young plantations. Further analyses showed that most Indonesian teak plantations are genetically related to Laos, Thailand, and Myanmar provenances. We conclude that there is a weak genetic structure on teak plantations among the regions, which indicates that most plantations were established using plant materials from a specific part of the natural teak distribution. Information regarding the genetic diversity and structure of plantation forests should be taken into account when making future plantation programs.

柚木（Tectona grandis由于其木材的实用性和价值，已在70个热带国家广泛种植。这种树种是在100多年前引入印度尼西亚的，在爪哇岛上发现了面积达120万公顷的大型人工林。但是，目前关于这些树的遗传多样性和起源的信息很少。我们从爪哇岛的三个区域（东部，中部和西部）收集了植物材料，并在每个区域采样了跨越三个年龄类别的树木，以阐明爪哇岛柚木种植园的遗传多样性和结构。我们使用测序的多重ISSR基因分型法（MIG-seq）调查了柚木种植和克隆实验种群，并将遗传多样性和结构与源自印度，缅甸，泰国和老挝的天然柚木来源试验种群进行了比较。使用459个单核苷酸多态性（SNP）位点进行的分析显示，本地种源比印度尼西亚柚木人工林具有更高的遗传多样性。此外，老柚木人工林的遗传多样性要比年轻人工林低。进一步的分析表明，大多数印尼柚木人工林与老挝，泰国和缅甸的起源具有遗传相关性。我们得出结论，区域之间的柚木人工林遗传结构较弱，这表明大多数人工林都是使用天然柚木分布特定部分的植物材料建立的。在制定未来的人工林计划时，应考虑有关人工林遗传多样性和结构的信息。