Arundinaria gigantea (river cane), a native bamboo species, was once abundant in river valleys of western North Carolina. Cane stands are now a rare ecosystem due to land use changes, but restoration efforts are underway. River cane reproduces mainly rhizomatously. Sexual reproduction is often characterized by gregarious flowering, followed by death of the flowering culms and possibly of the attached rhizomes. Suggestions have been made in the literature that clusters of flowering culms are monoclonal, but this has not been tested. In this study, leaves were sampled from sterile and fertile culms along transects from two stands in Jackson and Swain counties, North Carolina. Amplified fragment length polymorphism (AFLP) fragments were generated for these samples using three primer pairs. Most of the resulting AFLP fingerprints generated were not identical; however, using a threshold dissimilarity technique, we estimated the probable number of clones in our samples. The majority of fertile culms within a stand were determined to be monoclonal and distinct from some, but not all, of the sterile culms. Cluster analysis confirmed that most of the fertile culms within each stand were more genetically similar to one another than to the sterile culms, and that the two different stands had distinct sets of genotypes, with no genotype overlap between stands. On the basis of these findings, to maximize clonal diversity and minimize the impact of culm loss after flowering, restoration projects should use propagules collected from multiple stands and from multiple localities within a stand.