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Santalum spicatum (R. Br.) A. DC is a West Australian sandalwood species highly valued for the sesquiterpenerich oil in mature heartwood. The oil composition, particularly levels of the valuable sesquiterpenoids alpha- and beta-santalol and the allergenic E, E-farnesol, are known to vary across its natural distribution. Our study investigated associations of oil characteristics in 186 S. spicatum trees in semiarid and arid regions of Western Australia with genetic structure, environmental parameters and morphological features. We found associations between oil composition and genetic structure, as well as between oil composition and environmental factors. Analysis of individuals using STRUCTURE revealed two major genetic clusters (K = 2), comprising trees from the arid north clustered together, and the semiarid south-west clustered separately. Mantel tests revealed a significant association between oil characteristics and genetic distance (r = 0.129, P = 0.02). There was considerable variation in the growing environment of S. spicatum. An Adonis test showed a significant association between oil composition and provenance (P = 0.001) and between oil composition and soil type (P = 0.002) but not oil composition and other environmental characters. Soil type was significantly related to santalol and E, E-farnesol content. No significant associations between oil composition and morphological features were identified.