Cultivated potato is highly heterozygous and reports suggest extensive population level diversity. However, there are conflicting descriptions of the relationship between wild and cultivated diversity in the Solanum section Petota. This is in part because while cultivated US potato is tetraploid, wild potatoes are primarily diploid, and ploidy affects estimations of diversity. Furthermore, cultivated US potato is shaped by a history of extensive introgression from wild species. It is unclear if this is part of a larger pattern of interbreeding within section Petota or a unique feature of the cultivated potato genome. In an effort to quantify and describe the relationship between diversity in wild and cultivated potato we have genotyped a cross section of potatoes from the US potato genebank in Sturgeon Bay, Wisconsin using genotype-by-sequencing. This data set includes 54 diploids from seven taxa, four cultivated and three wild, and 548 tetraploids from two cultivated taxa. Even using measures accounting for ploidy differences we observe almost twice as much heterozygosity in tetraploids (HO=0.273) as in diploids (HO=0.134). However, expected heterozygosity which reflects population level diversity is much closer in diploids (HS=0.291) and tetraploids (HS=0.349), indicating substantial inbreeding in diploid potatoes (GIS=0.541). High inbreeding is consistent with the observation that diploid species with low observed heterozygosity are nonetheless segregating for a variety of phenotypes of interest to breeders. Clarifying how diversity is partitioned in wild and cultivated germplasm as well as patterns of admixture among these populations will inform breeder decision making around introgression breeding.