Solidago houghtonii Torrey & A. Gray ex Gray is a federally threatened polyploid plant species likely of hybrid origin. Several hypothesized combinations of parental species have been suggested but none have been phylogenetically tested. Additionally, it is unclear whether the species is of single or polytopic origin. To study the evolutionary history of S. houghtonii we sequenced four noncoding cpDNA loci (accD-psaI, psbA-trnH, trnL-trnF, rps16-trnQ), and the ITS and 3′ETS regions for four accessions of S. houghtonii, which span its geographic range, and 25 other species of Solidago including all sympatric species. Polymorphisms within the direct nrDNA sequences of all S. houghtonii accessions indicated the presence of multiple homoeologue types. These were separated by molecular cloning of the 3055 bp 3′ETS — ITS region, allowing us to positively link the ETS and ITS homoeologue types. Phylogenetic analyses of the nuclear and chloroplast datasets revealed incongruent topologies. Analysis of cloned nrDNA sequence data indicated that S. riddellii, S. ptarmicoides, and S. ohioensis have contributed to the nuclear genome of S. houghtonii. Analysis of cpDNA sequence data revealed the presence of multiple insertions/deletions that are shared by all accessions. The unique pattern of cpDNA indels was also recovered in S. gigantea. Phylogenetic analysis of the cpDNA sequence data and coded indels indicate S. gigantea is the maternal genome donor. However, we did not recover a S. gigantea nrDNA sequence type. Taken together, these data reveal both a single origin and a complex pattern of reticulation that is consistent not only with the hypothesized allohexaploid nature of this species, but also with chloroplast capture of cpDNA from an unexpected source through introgression.