Genetic diversity of all three extant species of the Hawaiian endemic tree genus Kokia was examined using analyses of RAPD markers. All three species are federally endangered, two (K. cookei and K. drynarioides) critically so, and one (K. kauaiensis) is rare but with several populations. Samples extracted were PCR amplified with 10 primers to yield 115 genetic markers. Analyses indicate that genetic variation is present in all three species; a surprising result given that K. cookei survives only from self-fertilized propagules of the single surviving individual that was grafted on to the root stock of a related species, K. drynarioides. Principal coordinates and cluster analyses based on RAPD markers indicate that although K. kauaiensis has substantial genetic variation, samples are clearly separate from the other two species of the genus. In contrast, K. cookei and K. drynarioides collections are more similar but still distinguishable when analyzed separately. Presence of substantial genetic variation lends optimism to the eventual recovery of K. kauaiensis through conservation efforts. Combinations of RAPD primers are suggested that reveal diagnostic alleles for each of the three extant species and can thus be used for species identification.