Hibiscus section Muenchhusia is a North American taxon with five species as recognized in the most recent taxonomic revision: H. coccineus, H. dasycalyx, H. grandiflorus, H. laevis, and H. moscheutos. To investigate the monophyly of Hibiscus section Muenchhusia, its relationship to other Hibiscus species, and the phylogenetic relationships among its species, DNA sequence data were obtained. To investigate the placement of section Muenchhusia within Hibiscus, chloroplast ndhF gene and rpL16 intron sequences were generated and added to a recently published dataset. To investigate relationships within section Muenchhusia three DNA sequence data sets were generated: a non-coding region of the chloroplast genome (rpL16 intron), nuclear ribosomal ITS, and a nuclear gene encoding granule-bound starch synthase (GBSSI). Analyses of ndhF rpL16 data indicated that section Muenchhusia is indeed monophyletic and is embedded in a clade that includes representatives of Hibiscus section Trionum sensu lato plus other genera segregated from Hibiscus (Abelmoschus, Fioria), and the tribe Malvavisceae. Within section Muenchhusia little to no phylogenetically informative variation was detected in the ITS or rpL16 sequences. The GBSSI data, on the other hand, provided sufficient information to resolve relationships among species. The species of section Muenchhusia fall into two primary clades, one consisting of H. grandiflorus and H. moscheutos sensu lato, the other including H. coccineus, H. dasycalyx, and H. laevis. These phylogenetic data corroborate earlier biosystematic studies that also placed the species into these same two groups. Sequence polymorphism was observed in one accession each of H. dasycalyx and H. grandiflorus and resolution of the underlying alleles indicates that gene flow has occurred from H. moscheutos into both H. dasycalyx and H. grandiflorus.