In a recent morphometric analysis of the Gonolobus complex (subgenus Gonolobus) in the southeastern United States, we found former specific concepts untenable as stated, as the diagnostic characters could not consistently assign individuals to one of two groups. However, our analysis showed a strong geographical component to the distribution of individuals delimited by uniformly and multicolored corollas, which we used as a basis for suggesting that two entities do appear to exist in the Southeast that may deserve recognition at some taxonomic rank. In the present study, we performed analysis of Inter-Simple Sequence Repeats (ISSR) to assess whether the two entities are genetically differentiated and, if so, to what level. We also conducted a cladistic analysis of morphological characters of the subgenus to determine whether the entities emerge as closest relatives. Our ISSR results showed substantial genetic differentiation at 18 loci between the two entities, although no fixed differences between them were detected. At 7 loci, the frequencies of band presence are significantly higher in the multicolored corolla group (MCCG) than in the uniformly colored corolla group (UCCG). At 11 loci they are significantly higher in the UCCG. Nineteen bands are unique to the MCCG, although at various frequencies (3.5–39.0%), whereas only a single band is unique to the UCCG, suggesting that the latter possesses a subset of the MCCG gene pool and is likely a derivative of it. Analysis of 61 parsimony-informative characters using Neighbor-Joining (NJ) and Unweighted Pair-Group Method using Arithmetic means (UPGMA) did not resolve the two groups, consistent with the view of a single species. In a parsimony analysis of morphological characters of 14 species of the subgenus, the two groups consistently appear as closest relatives. This evidence indicates that the complex represents a single evolutionary lineage with two incompletely differentiated morphological subgroups. On the basis of these results, we propose to treat the MCCG and UCCG as two varieties of Gonolobus suberosus. Gonolobus granulatus Scheele is neotypified in association with the required new combination for the UCCG variety. A key to the infraspecific taxa is provided.