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 diver...