AbstractPolygonella macrophyllaSmall is a rare, perennial, primarily gynodioecious plant species endemic to a narrow zone of coastal sand pine scrub habitat along the Gulf of Mexico from Carrabelle, Florida, to Gulf Shores, Alabama (U.S.A.). The species is comprised of a crimson‐red flowered form (“rubra”), known from only two populations at the eastern distributional limit of the species, and a white/pink flowered form ("alba") represented by several populations throughout the remainder of the range of the species. An electrophoretic investigation revealed that commonly used measures of gene diversity are very close to expected values in “rubra” given the combination of ecological attributes displayed by the species; however, gene diversity in “alba” is much lower than expected. Population differentiation is high, with estimates of the coefficient of gene differentiation (GST) indicating that more than 30% of the diversity is among populations. Lack of gene flow among populations, estimated to be at most 0.6 migrating individuals per generation for the species, is a likely cause of greater population differentiation. High inbreeding, detected both within populations and within the species, is suggestive of high rates of self‐fertilization in hermaphroditic plants and/or biparental inbreeding in sm