The restoration of native vegetation after the eradication of invasive alien species is an important step in the conservation of the threatened flora and fauna of the Bonin Islands. Terminalia catappa is one of the native woody species that can be useful for tree planting aimed at confirming rapid recovery of coastal vegetation. The investigation of the genetic structure within the species is required to avoid artificial modifications of genetic structure.

Leaf samples were collected from a total of 673 individuals in 22 populations chosen to represent the distribution range of T. catappa in the Bonin Islands. Their genotypes were determined using 11 microsatellite markers. Gene diversity ranged 0.297 - 0.534. The global F_ST value among 22 populations was 0.04, and the relationship between pair-wise F_ST and geographic distances was significantly positive. Both the STRUCTURE analysis and the principal coordinate analysis suggested that T. catappa populations in the Bonin Islands could be largely divided in the following two clusters: the one is dominant in the Muko-jima and Chichi-jima island groups, and the other is dominant in the Haha-jima island group. These findings would be useful for the establishment of sound restoration strategy for the coastal vegetation of the Bonin Islands.