We present the study of the genetic diversity and structure of a tropical tree in an insular system, using nuclear and chloroplastic microsatellites. Santalum austrocaledonicum is endemic to the archipelago of New Caledonia and is exploited for oil extraction from heartwood. 431 individuals were analysed for 8 nuclear microsatellite loci and 165 individuals for 3 chloroplast microsatellite loci. Both markers revealed that the genetic diversity was low in the most recent islands, the Loyautés, and high in the oldest island, Grande Terre, as well as the closeby small Ile des Pins. A strong genetic differentiation among all populations was observed, and the amount of differentiation increased with geographic distance in Iles Loyauté and in Grande Terre. At both population and island levels, island age and isolation seem to be the main factors influencing the amount of genetic diversity. In particular, populations from recent islands had large average Fis with nuclear microsatellites, that could not be entirely explained by null alleles or a Wahlund effect. This result suggests that, at least in some populations, selfing occured extensively. Conclusively, our results indicate a strong influence of insularity on the genetic diversity and structure of Santalum austrocaledonicum. (Texte intégral)