Technical Abstract: Recent genomic studies have drastically altered our knowledge of polyploid evolution. Data from genomics suggest that almost all angiosperms, perhaps even all plant groups have experienced one to several rounds of genome duplication. Polyploids regularly experience preferential expression or loss of duplicated genes, homoeologous recombination, and a variety of epigenetic changes. Polyploidy can drastically increase, in a single event, genetic diversity that can be reshuffled in a variety of ways to increase the ecological and physiological adaptation relative to their ancestors. Certain polyploid species have been shown to have arisen multiple independent times. Wild potatoes (Solanum section Petota) are a highly diverse group of about 100 species widely distributed throughout the Americas. Thirty-six percent of the species in sect. Petota are entirely or partly polyploid and the series is ideal to study polyploid evolution. We here conduct a DNA sequencing study, using six nuclear orthologs, of 54 accessions of 11 polyploid wild potato species, and 37 diploid species representing their possible ancestors. The present study documents considerable genomic complexity in potato polyploids to include new alleles not found in prior studies, clades not recovered before, apparent allele loss, and multiple origins. It adds to a growing body of evidence showing considerable complexity in polyploids, and is of considerable practical benefit to the classification and use of this economically important group.