Solanum section Petota is taxonomically difficult, partly because of interspecific hybridization at both the diploid and polyploid levels. There is much disagreement regarding species boundaries and affiliation of species to series. Elucidating the phylogenetic relationships within the polyploids is crucial for an effective taxonomic treatment of the section and for the utilization of wild potato germplasm in breeding programs. We here infer relationships among the potato diploids and polyploids using nitrate reductase (NIA) sequence data in comparison to prior plastid phylogenies and: 1) examine genome types within section Petota, 2) show species in the polyploid series Conicibaccata, Longipedicellata, and in the Iopetalum group to be derived from allopolyploidization, 3) support an earlier hypothesis by confirming S. verrucosum as the maternal genome donor for the polyploid species S. demissum as well as species in the Iopetalum Group, 4) demonstrate that S. verrucosum is the closest relative to the maternal genome donor for species in ser. Longipedicellata, 5) support the close relationship between S. acaule and diploid species from series Megistacroloba and Tuberosa, and 6) show the North and Central American B genome species to be well distinguished from the A genome species of South America.