Experimental and comparative evidence implies that homoploid hybrid speciation is a reproducible process, mediated in part by ecological selection. Here, molecular data from the chloroplast genome and 17 nuclear microsatellite loci were employed to determine whether a well-documented homoploid hybrid species, Helianthus paradoxus, has arisen multiple times. Helianthus paradoxus is ecologically divergent from its parental species, and has a disjunct geographic distribution consistent with multiple origins. The molecular data, however, strongly support a single hybrid origin. First, all sampled populations of H. paradoxus are fixed for a single chloroplast DNA (cpDNA) haplotype, whereas local populations of both parental species, H. annuus and H. petiolaris, have multiple cpDNA haplotypes. Second, H. paradoxus populations form a single, well-supported clade (99.8% bootstrap support) in a neighbor-joining tree based on microsatellite allele frequencies. The microsatellite data also tentatively place the origin of H. paradoxus between 75,000 years and 208,000 years before present, indicating that anthropogenic disturbance likely did not play a role in the formation of this species. Finally, the genetic structure of this species is not consistent with passive riparian dispersal, which has been suggested for other wetland plant species, but may be explained by dispersal mechanisms implicated for H. annuus, such as large migratory mammals.