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Proper taxonomic classification of species is essential to the conservation of rare species to ensure that they garner needed protection. This study was undertaken to determine relationships among the Hawaiian representatives of Cryptocarya. This genus is represented in Hawai‘i on the islands of Kaua‘i and O‘ahu, where it is currently classified as a single species (C. mannii) and not considered endangered. It had previously been recognized as two species, C. mannii on Kaua‘i where it is relatively abundant and C. oahuensis on O‘ahu. O‘ahu plants have been in decline since their discovery over 100 yr ago and now only one naturally occurring plant is known. RAPD analysis demonstrates that populations on Kaua‘i are genetically distinct from those on O‘ahu. Sequence analysis of nuclear (ITS) and plastid (trnK intron) gene regions shows distinctions among plants from different islands (ITS: four or five base substitutions plus one repeat length difference; trnK intron: one base substitution plus one repeat length difference). Differentiation identified here is comparable with that of some con-generic species elsewhere and is consistent with recognition of C. oahuensis and C. mannii as separate species. Both species are members of the Asian-Australian clade in a broader phylogenetic analysis. Morphological traits that distinguish each species are examined, and a key to the species is provided. Conservation measures to protect the critically endangered C. oahuensis are discussed.