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AbstractDalbergia latifolia is commercial tropical tree species known for its beautiful heartwood, mainly used for furniture and musical instrument. High market demand has put concerns on its sustainability and conservation aspects in Indonesia. Ninety-five specimens of D. latifolia were collected from eight populations of Java, Lombok, and Sumbawa Island to study intraspecific variability and diversity using SRAP. One hundred and eighty SRAP loci with 54.03% ± 4.35% polymorphism obtained from PCR amplification of 10 primer combinations, with the average PIC for these primers of 0.28. Genetic diversity and variability measures were calculated using GenAlEx software indicating a relatively low-mid level of percentage of polymorphic loci (PPL) (54.03%), effective number of alleles (Ne) (1.255), Shannon information index (I) (0.242), and heterozygosity (He) (0.156) on average. The highest value (I = 0.309, He = 0.196) was observed in population P2CJ (Central Java), followed by West Java of P1WJ (I = 0.300, He = 0.191) and West Sumbawa of P7Wsumb (I = 0.257, He = 0.169), while the lowest (I = 0.202, He = 0.129) was found in West Lombok (P4WL). The genetic relationships were measured from genetic distance and identity from the two-pairwise calculation, PCoA, and STRUCTURE analysis. The relative homologous population is found between populations Central and West Java of P2CJ and P1WJ (Nei uD = 0.031), suggesting these populations have the same origin and formed one population, while the most distinct (Nei uD = 0.157) was recorded between Sumbawa regency (P6Sumb) and East Java (P3EJ). The results from PCoA showed that all individuals are placed in three groups almost in accordance with their respective islands, i.e. a group comprised inclusively trees from Sumbawa island, a group of Lombok and some Central Java trees, and a group of trees from Java with the exclusion of some trees of Central Java that were clustered with trees from Lombok island. This result was also supported by STRUCTURE analysis, which showed that Sumbawa, Lombok, and West-East Java populations formed their respective clusters, and Central Java population contains a mixture of West-East Java and Lombok populations. This may suggest evidence of complex origin, thus needing further study to clarify. It is recommended that the populations with the highest value of genetic diversity (Central and East Java) are to be maintained as the source of the gene pool for genetic enrichment programs.