Diervilla is an eastern North American genus sister to the eastern Asian Weigela within subfamily Diervilloideae of Caprifoliaceae. Diervilla contains two Southeastern USA endemic taxa, D. sessilifolia and D. rivularis, and one more northern taxon, D. lonicera, that also has a relictual distribution in high elevations of the Southern Appalachians. While three species of Diervilla are often accepted in floras and checklists, confusion among what constitutes the species still exists and has led to questionable identification in the field and on herbarium specimens and uncertainty about species distributions. The difficulty lies in high morphological similarity between the Southeastern endemics, as well as identification keys using adjacent quantitative character measurements and few discrete characters to distinguish among all three taxa. Previous phylogenetic analyses using sequences of the nrITS and noncoding cpDNA regions were unable to resolve relationships among the taxa or even to determine whether samples from multiple populations of each taxon were monophyletic due to lack of informative variation. To clarify the taxonomy and relationships within Diervilla, I obtained samples from multiple populations of each taxon throughout their ranges, examined and measured morphological traits on herbarium specimens, and sought new characters to aid in species identification and delimitation. I generated a ddRAD-Seq dataset from field and herbarium specimens to try to obtain a better resolved phylogeny and study the potential for incomplete lineage sorting or admixture, which might signal lack of species differentiation or post-speciation introgression. RAD sequences were assembled and aligned de novo, and resulting datasets were used in maximum likelihood and quartet sampling phylogenetic analyses, as well as Structure admixture analyses. Morphological data were subject to multivariate analyses. As a result, the three named species, D. sessilifolia, D. rivularis, and D. lonicera were resolved into clades with high bootstrap support and distinguished by a newly described, discrete morphological character, twig hair type. Other, often overlooked, qualitative traits can help distinguish taxa, while quantitative traits are often overlapping. Diervilla sessilifolia and D. rivularis are confirmed as closely-related sister species. Structure results show some admixture among all three species, either as a result of recent shared ancestry or hybridization, possibly following Pleistocene range contraction and expansion. This study demonstrates the utility of genome-wide RAD-Seq data to resolve relationships among closely related taxa and the need to critically assess morphological characters in groups with taxonomic confusion.