The genus Amorpha is a North American endemic in the family Fabaceae comprising ~20 species. The genus is characterized by the absence of the floral keel and wing found in most papilionoid legumes, dramatic morphological variation, and the ability to occupy various habitats. A. fruticosa has the broadest range of all species encompassing the distribution of the genus. The majority of other Amorpha taxa occur in various habitats, including riparian corridors, prairies, and savannas. A. fruticosa has at least 39 synonyms, suggesting taxonomists have noticed enough morphological variation in this species to merit the naming of new taxa. This taxonomic confusion leads us to question if A. fruticosa is a single species with high morphological plasticity, or if hybridization between species results in novel morphologies or preference for diverse and novel habitats. Using a combination of morphological analysis, ecological niche modeling, and whole-chloroplast genome sequencing for 80 accessions of Amorpha, we address these questions focusing on A. fruticosa, A. glabra, A. nitens, and A. schwerinii, the primary species of Alabama. Our data suggestA. fruticosais non-monophyletic and morphologically diverse. We also describe population-level chloroplast diversity across the southeastern US with a focus on identifying novel chloroplast haplotypes. The chloroplast phylogeny will further elucidate the relationships of this genus and allow us to develop a better understanding of species diversity, not just across the Southeast, but in general, for morphologically diverse species, like A. fruticosa