Abstract
Swietenia macrophylla has been planted across Viti Levu and Vanua Levu, Fiji since the 1960s, establishing roughly 40,000 ha from imported seed of multiple Central and South American countries. The estate is a land race in formation and an unintended ex situ holding of a CITES Appendix II species, yet its genetic composition is uncharacterised. We quantified genetic diversity within and among Fiji’s plantation populations, characterised population genetic structure, and tested for spatial differentiation, expecting a priori that one to two generations since planting would be too few for isolation by distance to emerge. We genotyped 83 individuals from seven cohort-stratified populations at three Viti Levu sites using DArTseq™. After filtering (call rate≥0.80, reproducibility≥0.96, MAF≥0.05), 25,850 SNPs were retained. All individuals carried unique multilocus genotypes. Observed heterozygosity was 0.168–0.202 and inbreeding coefficients 0.092–0.173. Global Weir–Cockerham FST was 0.0023, with AMOVA attributing 99.2% of variation to differences among-individuals within populations. Neither a Mantel test (r = 0.008, p = 0.378) nor dbMEM analysis (p = 0.159) detected isolation by distance, as expected. Diversity is retained across sites and recruitment cohorts, and differentiation is negligible—the pattern predicted by a broad, multi-provenance founding sample rather than by contemporary gene flow. Suva carries the greatest allelic richness and 1233 private alleles, a priority for ex situ conservation. Harvesting rules should weigh relatedness rather than phenotype alone to prevent genetic erosion under commercial harvesting. The recruitment sustaining this gene resource also marks an exotic reproducing unaided on a high-endemism archipelago.