Santalum macgregorii (sandalwood), which is endemic to the southern part of Papua New Guinea (PNG), has been heavily exploited for its fragrant heartwood and is classified as threatened across its natural range. Domestication and smallholder agroforestry offer the means to preserve remaining diversity. This study was undertaken to understand the extent of remaining natural variation to support the species's conservation and domestication. We evaluated morphological, heartwood and essential oil characters in 126 S. macgregorii trees in five populations (districts) in PNG's Central, Gulf and Western provinces. The heartwood oil of this species is characterised by extreme tree-to-tree variation in key fragrant compounds. Proportions of individual compounds range from negligible to high for (Z)-α-santalol (0.5-51%), (Z)-β-santalol (0-24.2%), (Z)-nuciferol (0-40.5%) and (Z)-lanceol (0-72%). Despite the wide variation found within populations, an ordination of seven oil constituents revealed broad provenance-based variation in which trees from the eastern provinces (i.e. Central and Gulf) were more influenced by (Z)-nuciferol content and the trees from the Western Province site were more strongly influenced by (Z)-lanceol. The driver of this variation was the different associations between oil constituents, with (Z)-α-and (Z)-β-santalol both negatively correlated with (Z)nuciferol for sites in the eastern provinces and (Z)-lanceol in Western Province. No evidence of distinct chemotypes was found, with continuous variation demonstrated across all major oil constituents. Of the trees surveyed with a basal diameter of >10 cm, 79% had heartwood. Mean heartwood percentage was 15.8% of basal area, with no significant differences between sites. Significant tree-to-tree variation in heartwood percentage (0-61%) was found. A modest positive correlation was found between stem and heartwood diameter (r = 0.39). Heartwood percentage and heartwood oil quality varied independently and, therefore, independent selection of these traits may be required for their simultaneous improvement. The population in Western Province is non-contiguous with those in the eastern part of the species distribution. It also has a distinct phenotype based on oil composition, leaf shape, flower colour and potential reproductive failure. It is possible that sandalwood in Western Province is more closely related to the proximal populations of S. lanceolatum in Cape York Peninsula, Queensland, than the more distant populations of S. macgregorii in PNG. While these phenotypic features do not necessarily discriminate a new species, molecular genetic research is required to determine the potential existence of a cryptic species of sandalwood. The implications of the variation found in S. macgregorii are discussed with respect to its domestication and conservation.