Eucalyptus urophylla is one of the most economically important species in the world due to its wood quality and tolerance to water stress. Understanding the genetic composition at the population level of this species is essential for the sustainable and efficient management and utilization of its genetic resources. This study describes the genetic diversity and population structure of E. urophylla from progenies collected on four islands in Indonesia (Wetar, Timor, Lembata, and Adonara) and conserved ex situ in Brazil. A total of 658 open-pollinated adult individuals from 17 populations were genotyped using 5,374 SNP markers. Analyses of diversity (observed heterozygosity, \({H}_{o}\) , and expected heterozygosity, \({H}_{e}\) ), population hierarchical levels ( \({F}_{ST}, {F}_{IT}, \text{and} {F}_{IS}\) ), effective population size ( \({N}_{e}\) ), admixture, PCA, and Neighbor-Joining dendrogram were conducted. The populations showed greater genetic differentiation at the island level ( \({F}_{ST}\) =0.042). The estimates of genetic diversity were moderate, with \({H}_{o}\) ranging from 0.38 to 0.43, and higher than \({H}_{e}\) , which ranged from 0.30 to 0.33. The sublevels \({F}_{IS}\) and \({F}_{IT}\) showed negative estimates, indicating a high proportion of heterozygous individuals in the populations and a negative intraclass correlation, showing that alleles were more related among than within populations. There was low genetic differentiation among populations ( \({F}_{ST}\) <0.05). The analyses showed a clear and significant separation of three genetic clusters. The observed genetic diversity and structure ensure that ex situ conservation can be effectively carried out, preserving and exploring the genetic variability found in natural populations.
