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Kokia (Malvaceae) is a tree genus consisting only of three endangered and one extinct species endemic to the Hawaiian Islands. Morphological and molecular population analyses suggested conflicting hypotheses as to colonization and dispersal among the Islands. To resolve this, 12 nuclear and four chloroplast gene regions were sequenced and compared to establish phylogenetic hypotheses and to make biogeographic inferences. Seven gene regions yielded phylogenies consistent with the progression rule hypothesis suggesting dispersal from older to younger islands, seven other gene regions were equivocal, and two weakly supported an alternative phylogeny. Combined analyses of all genes strongly supported the progression rule hypothesis, with initial colonization to Kaua‘i, or possibly an older and now submerged island, with subsequent dispersal to O‘ahu, Moloka‘i, and Hawai‘i Islands. Morphological characters plotted onto the molecular phylogeny suggested that many morphological traits are plastic or nonhomologous. Our study illustrates the perils of evaluating relationships among widely divergent taxa using morphological characters.