Santalum (sandalwood) spp. are hemi-parasitic trees, the heartwood of which produces valuable aromatic oil. There appears to be a significant commercial opportunity for establishment of a planted sandalwood resource. However, lack of basic biological knowledge is one constraint on such development. The study reported here addresses one such constraint. Controlled pollination using 13 genotypes of Santalum lanceolatum was undertaken to elucidate (i) self-incompatibility (ii) intraspecific cross-compatibility in the species, and (iii) interspecific cross-compatibility with S. album and S. austrocaledonicum. S. lanceolatum may be considered to have a facultative allogamous (incomplete outbreeding) breeding system. This study found variation between genotypes in the level of putative self-incompatibility: some (20%) were found to set seed following self-pollination, while the remaining 80% had no seed development with such pollinations. However, a significantly greater proportion of genotypes developed seed following intraspecific cross-pollination (62%) compared with self-pollination (20%). While total geographic isolation and significant morphological divergence exists between S. lanceolatum with each of S. album and S. austrocaledonicum this study found no indication of reproductive barrier(s) between them, indicating potential for use of interspecific hybridization in genetic improvement, but also suggesting the potential of undesirable gene flow between native and introduced species. © 2011 Springer Science+Business Media B.V.