Sesbania tomentosa (Fabaceae) is an endemic flowering plant primarily adapted to coastal strand and dry lowland habitat in the Hawaiian Islands. Previous studies have attempted to delineate distinct taxa from among the extant populations. In the most recent treatment of Hawaiian Fabaceae, however, S. tomentosa was recognized as a single polymorphic species with two forms. To readdress issues of taxonomy, the present study utilized microsatellite marker variation and DNA sequencing to discriminate Hawaiian Sesbania populations. While there was no DNA sequence variation among species for ITS or TRPT gene regions, microsatellite analysis found a highly differentiated population structure at the nine loci sampled. Bayesian genetic clustering assignments and associated private alleles occurred in a distinct phylogeographic pattern. As a result, three distinct genetic groups were identified corresponding to islands of origin: populations from Nihoa, Kaua‘i, and O‘ahu (group 1), populations from Maui, Kaho‘olawe, and Moloka‘i (group 2), and populations from Hawai‘i Island (group 3). The extremely varied yet randomly overlapping morphologies among the populations suggest widespread convergent evolution has occurred and precludes any subspecific taxonomic designations. We interpret the high levels of genetic marker and morphologic differentiation exhibited by Hawaiian Sesbania to be a product of the plant’s reproductive ecology and its influence in sub-structuring populations on a small geographic scale. Efforts toward preservation of the wide range of distinctive appearing morphotypes should continue, facilitated by the natural tendency of the plant to maintain a more or less fixed state of certain traits within populations.