The forest tree Santalum insulare is endemic to the archipelagos of eastern Polynesia and is threatened by important anthropic pressures. In order to investigate the genetic diversity and structure of this species, we developed eight pairs of primers for nuclear microsatellites. One hundred and sixty-two individuals distributed in 10 islands were analysed. These loci were all polymorphic and displayed three to 15 alleles per locus. Significant Hardy–Weinberg deviation was detected and interpreted as a result of Wahlund effect. These markers constitute an efficient tool in investigating the genetic patterns of S. insulare populations.