The Hawaiian Islands are home to a quarter of the named diversity of sandalwoods in the genus Santalum. There has been considerable confusion on how to best interpret the variation patterns of the red-flowered Hawaiian sandalwoods, S. freycinetianum and S. haleakalae,
and particularly of the endangered S. freycinetianum var. lanaiense in an appropriate taxonomy. In this study, nrDNA (ITS, ETS) and cpDNA (3′ trnK intron) sequence, microsatellite, and morphological data are integrated to appropriately revise the taxonomy of this
group by better understanding the genetic and morphological diversity within and between populations. Results reveal that populations of S. freycinetianum from O'ahu are genetically distinct from populations on Moloka'i, Lana'i, and Maui. Santalum freycinatianum is now considered
only to occur on O'ahu. The East Maui endemic S. haleakalae intergrades morphologically and is not genetically distinct from populations of S. freycinetianum var. lanaiense based on the sequence and microsatellite data gathered thus far. We combine them here into a single
species, S. haleakalae, with two varieties (var. haleakalae and var. lanaiense, comb nov.). Lastly, examination of populations of S. freycinetianum var. pyrularium suggest it is best treated at specific rank as S. pyrularium. Some populations that
are sympatric with S. pyrularium and S. ellipticum in the coastal cliffs and valleys of northern Kaua'i, are morphologically similar to S. pyrularium but are more closely related to the white-flowered S. ellipticum clade according to both nrDNA and cpDNA data. However,
at least three synapomorphic sites in the nrDNA data indicate that its origin may have been the result of an ancient hybridization event with the red-flowered clade. The morphological characteristics of this inferred ancient hybrid lineage appear to correspond with the species S. involutum
described by H. St. John.